There is an NPC that I want to introduce soon, but I don’t want the PCs to be suspicious of her until a later big reveal that she is a major villain.
My game has a woman who is a noblewoman. Despite her low-status birth and life as a peasant, she would later be seen as a miracle child because of in-world lore related to a physical feature of hers. This allowed her to get many followers who helped push her into the ranks of lower-"nobility" as a baronetess. From there she manipulated her followers in order to make her actions seem more praise-worthy and honorable that she eventually was made a trusted adviser of the king's, granting her a formal nobility rank as a Countess and, as a result, allowing her to run her criminal operations more smoothly.
Okay, lore aside… She is an absolutely beautiful and cunning woman. She never lies because she doesn't ever have to thanks to her wording. She has a high charisma and wisdom, so if someone were to question her, she would always be multiple steps ahead of them so that she doesn't have to say anything that is false. That said, one of her quirks is that she tries to collect (Read: "Enslave"/"Own") anything that she finds to be unique or valuable and she sets her eyes on one of the PCs.
The villain’s introduction
The PCs just shut down a large part of the kingdom's slave trade. Slavery isn't illegal, but it is something the king is trying to edge out of their society. At the same time, he can't request people to shut down and deincentivise slavers lest he causes unrest in his nobility. He trusts Countess who he does not realize 1) owns many slaves that she keeps hidden in secret and 2) is the one in charge of the vast majority of the kingdom's slave trade; therefore, the king has invited Countess to the celebration of the PCs shutting down such a large aspect, freeing many slaves and getting them someplace safe. Publicly, the celebration is under the claim that the PCs found a lost artifact (which they do by chance) belonging to the royal family (and therefore the kingdom) by right and it's to honor their (the PCs') service to the crown. Everybody who is invited to this celebration are those whom the king trusts with the information relating to the true reason for the party, guests and staff alike.
At the party, Countess will try to seduce one of the PCs by putting a "love potion" of sorts into a drink which she will then offer her target. (I as the DM expect the player to succeed the DC to be unaffected by the immediate effects of the potion, so mentioning the potion is more "side information" than anything.) That said, when they are talking, I need to know how specifically to keep her from coming across as obviously suspicious since she will be directly approaching one of my players and will have a noticeable impact on him thanks to a very "Strahd von Zarovich"-style Charm skill while they are talking, regardless of if he drinks from the spiked glass or not.
My players are quite genre-savvy. When I do this, I expect them to figure out that she is suspicious, if not evil, but I want to avoid her being seen as even suspicious. What is the best way to do this while maintaining the story as intended? This is done through a homebrew system, but if you must, assume D&D's system. If you need my party's (the PCs, not the celebration,) information in order to answer this accurately, let me know.
How can I convince my players, not just the characters, that this evil character is actually good for a prolonged length of time until the final reveal?
A best answer will be almost entirely through minimal use of rolls and maximized use of story-telling. Rolling would just add to the suspicion and I don't want my players to even think they are on to me.
Don't roll for plot
There are lots of quality answers on this post but I'm going to try to address an issue that you mention in several comments. You said:
I'll challenge the "inevitably" part of that statement. You are the DM, players dictate their actions and you decided on the outcome. Roll only if required.
You are correct that continually rolling deception and charm checks behind the screen will raise suspicion. Even non-genre-savvy players will notice if you start playing one NPC different from all the rest. Instead, set static DCs for insight and perception checks against her, probably DC25 or higher if you don't want her to get caught. If the players/characters try anything that might see through her disguise, let them roll against this. Never ask them for the roll, if they don't think to check her out then you have already succeeded.
Something I try to live by when running games is: Never roll if you aren't prepared for both outcomes. This means that if your plot requires the players succeed at a certain point or it will ruin the whole session, they succeed, no roll required. It also means that when the NPC has to pass that stealth check to leave a foreboding note next to a sleeping PC, they succeed, don't bother rolling.
Hindsight is a natural 20
Do evil people constantly do large evil things? No, they do small everyday things that add up to an evil whole. A clever villain knows not to show their hand too early.
Craft your NPC such that no single action of their can be called into question on its own, but after the reveal the players can determine the clear path of evil actions. Some things you can try along this line:
Whatever you do you need to ensure that nothing the NPC does raises the eyebrows of your astute players. They are a master of hiding their true nature and their morals are beyond reproach. Szega's answer on playing her as almost two completely different NPC is great. The well-mannered noble could never be connected with the devious crime lord.
I'm not going to reveal how I've done this as a DM as the campaign is ongoing and I don't one of my players stumbling onto it. However I have also played in a game with a great DM that did this well.
It was a game of Shadowrun and the NPC in question was our boss (quest giver) Abby Road. At the start of the campaign the GM needed to show that Abby was far stronger than us. He didn't even bother rolling for attack or defense, we couldn't hit her and she couldn't miss us. (I'm not suggesting this by the way but it made the point.)
Initially all our missions were for good beneficial things for both us and our crew. Retrieving supplies, stopping rival crews, freeing the innocent that sort of thing. As the campaign went on there were a few missions that seemed questionable, but we trusted Abby because she looked after us from the start. She had gotten us out of a few bad scraps before and would never hurt us.
Time went by and our missions became even more suspect, we were breaking into important peoples home to steal documents, planting false evidence and destroying weapon shipments. We assumed this was a building tension in the world rather than the advancing machinations of a nefarious villain.
I will admit that I was a little suspect of this seemingly benevolent leader, but I was the only one and some of it stemmed from a personal disagreement my between my character and her (she gave me a beatdown early on) rather than actually knowing she was dodgy.
Eventually at the end of the campaign we came to a confrontation against the leader of the city that she had secretly been plotting to bring down with our help. In the reveal I turned against her and my party as they took her side and it lead to an epic final session.
The point of this story is that using these techniques the party were so convinced she was on the right side that even when it became clear she wasn't they still sided with her.