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.
The problem is that grammar is somewhat tied to meaning here. The position of an adjective in a sentence depends on its role.
When used attributively (to describe a noun), as stated in other comments and answers, the adjective comes before the noun:
All navigable rivers are being patrolled.
If you say:
All rivers that are navigable are being patrolled. (Others are not)
This can become:
All rivers navigable are being patrolled.
At first glance this doesn't really seem to change the meaning since:
rivers that are navigable = navigable rivers
Edit: But...
When an adjective comes after the noun it describes (like in the 3rd example), it functions as a postpositive modifier. Changing the position of the adjective (relative to the noun it describes) may bring a slight difference in the meaning of the sentence (the meaning of the word itself does not change!). When used postpositively an adjective connotes an ephemeral quality, one that is present at the moment, but doesn't always have to be. On the other hand, the adjectives used attributively may express either an ephemeral or a permanent characteristic, depending on the context. The difference between attributive and postpositive use of an adjective is explained in more detail in (the middle of) this post and in the comments.
Only some adjectives can be used both attributively and postpositively (while retaining the same word meaning), and these are the ones ending in -able and -ible (such as navigable). (But not even all of those - see later: responsible).
To cover another aspect (this is where grammar kicks in again): if an adjective is used predicatively (in a pattern: subject + verb + object + complement (here an adjective)) it would be in a sentence like this:
Signalisation on the banks made rivers navigable. (Or something like that, I'm not really an expert on rivers).
The upcoming event made people excited.
The meaning of some adjectives (when used as modifiers) changes depending on whether they are used attributively or postpositively. Some examples are: concerned, responsible, present etc. Neither navigable nor excited are among those. Here the meaning of the word itself changes and the difference can be determined by checking the dictionary definitions.
Best Answer
As indicated by narx's answer to a similar question on ELU (English Language & Usage, ELL's "sister site" aimed primarily at linguists, etymologists, and serious English language enthusiasts), only little can be used as an unqualified noun to mean a small amount (where adjectival small needs an explicit noun, such as amount or quantity).
The other interesting point made about little there is that in...
...the two sentences have almost opposite meanings - #1 implies you have at least some experience, whereas #2 implies very little (perhaps almost none). In fact, #1 is often used somewhat facetiously to imply you actually have a lot of whatever is being spoken of.
Apart from the above distinctions, there's also (as kiamlaluno points out) the fact that little often carries more "affectionate" connotations than small. And from BBC Learning English, little is more common in the sense not much when coupled with abstract nouns such as hope, chance, change, effect, use and point.
In most other contexts, there's little to choose between the two words. Use whichever you like.