The only way to be sure is to memorize. However, you can use guidelines to make the right choice 90% of the time or more.
If there is no compartment involved, you get ON it. (bicycle, motorcycle, skateboard, etc.) (Note: partial compartments, such as those of convertible cars or open-topped boats, count as compartments; pretty much anything where the vehicle at least partially surrounds you.)
Oddly enough, if the transportation is large enough to allow you to move around freely, you also get ON it. (Bus, train, large boat, passenger plane, etc; anything with an aisle or walkway.)
Otherwise, you almost certainly get IN it. (Car, personal aircraft, canoe, etc.)
Thus, you would get IN a speedboat, but get ON a cruise ship, even though both are boats and both are enclosed, because the speedboat is small enough that although you can probably change seats without difficulty, you can't really move around freely inside it.
As a counterexample, even though a van may be large enough that it does have an aisle and you can move around freely inside it, if you call it a van, you get IN it.
This is an area where usage has gradually changed. Historically, the preference was not to use any preposition at all between at a loss and what to do. But increasingly people now insert one of various alternatives including as to, for, over, regarding, to know, etc. And if this NGram is to be believed, the first of those is now the most common form...
There's no grammatical rule involved here - just idiomatic "custom and practice". Personally, I don't find any of OP's suggested of, at, or on acceptable, but all the alternatives graphed above seem at least "credible" to me (though like most people, I would normally use as to in this exact context).
Best Answer
“Decide for yourself” would mean you’re making the decision that is only for you. The consequences of your decision only affect you. For example: “I’m going to order chocolate ice cream, you decide for yourself what you want”
“Decide by yourself” means you’re making the decision on your own without anyone else. The decision may or may not affect others, but they don’t get a say in it. For example “I hear your suggestions, but I’m going to decide by myself what to do” or “the judge will decide by himself who will win the prize”
There are some cases where you could use either and they would be correct. But you couldn’t say “the judge will decide for himself who will win the prize” because the prize isn’t for him, it’s for someone else.