No, You cannot combine attacks with booming blade.
Both Booming Blade and Green Flame Blade say the following:
As part of the action used to cast this spell, you must make a melee attack with a weapon against one creature within the spell's range
This means that these cantrips do not require you to take the Attack action, they require you to take the Cast a Spell action.
If we look at extra attack, it is defined as:
Beginning at 5th level, you can Attack twice, instead of once, whenever you take the Attack action on Your Turn.
No Attack action is taken, so no extra attacks can be used. Additionally, two weapon fighting states:
When you take the Attack action and attack with a light melee weapon that you’re holding in one hand, you can use a bonus action to attack with a different light melee weapon that you’re holding in the other hand.
Again, no attack action is taken, so you cant use a bonus action to make an off hand attack.
In your scenario, you can cast hunter's mark or hex, and then the hit from the booming blade will trigger those effects, as well as sneak attack (if the conditions are met), but you will be unable to make more attacks after that.
Action surge gives you another whole action, which you can use to cast a spell, like Booming Blade which will give you one more attack, or if you just use a regular attack action, extra attack and two weapon fighting could apply.
The spell does exactly what it says it does, and no more
Choose one object weighing 1 to 5 pounds within range that isn't being worn or carried.
This means that you can't use it on an item that you are carrying, so you can't use this spell on the crossbow bolt hidden in your sleeve. You probably can't cast it on a crossbow bolt anyway, since it most likely weighs less than a pound. However, you can get around this limitation by casting it on nearby objects, like rocks, or by dropping the item you want to catapult first.
Additionally, you don't get any critical or sneak attack damage because this spell requires a saving throw, not an attack roll. This question explains why there are no critical hits on spells that require saving throws. Similarly, the Assassin's Assassinate feature only applies to attack rolls. Thus, you only get the 3d8 damage from the text of the spell.
Finally, it's reasonable for your DM to rule that sharp items could deal piercing damage, but that would be a houserule. Officially, every item flung by Catapult deals bludgeoning damage--if that's what your DM has decided, he is supported by the rules.
Whistling is probably not an appropriate somatic gesture
PHB 203 states,
Spellcasting gestures might include a forceful gesticulation or an intricate set of gestures. If a spell requires a somatic component, the caster must have free use of at least one hand to perform these gestures.
Which suggests that spells that require somatic component require hand motions. Whistling is arguably a verbal component, rather than somatic.
This does not work as you have described in your question. Surprise can only happen in the first round, and is based on stealth. It doesn't mean that it applies when the enemy is surprised to find out that you're actually a magic user. Additionally, surprise is a state; a character is either surprised or is not.
Your assassin auto-crit ability only triggers when you have the drop on an enemy and they have not succeeded on a Wisdom (Perception) check to spot you. During the first round of combat, you will have advantage against any enemy who is surprised, and any hits against them will automatically be critical hits.
In your scenario, you would need to cast your spell in the first round for this to apply, but I will note that your crossbow attack + Hex damage would be counted as a critical if the enemy were surprised.
Subtle spell does nothing to help your surprise in this situation.