Your biggest concerns should be:
weight
size
CFM
how is it powered
Unfortunately, there are tradeoffs across the board
the lightest compressors (electric) will require a huge current draw off the boats electrical system, thus requiring a good sized onboard generator
midrange weight compressors are gas powered, but, that means you have to have another storage system for gas...
chances are the boat has a smallish diesel engine, which means there is already a diesel supply aboard the boat, however diesel compressors are the heaviest...
CFM - most smallish compressors in the 3-4 CFM range will fill a single tank (80 CF, from 500 to 3000 psi) in 20 minutes, so for a pair of divers, thats 40 minutes, but for any more it gets to be a long time to fill... this can be offset by having a single bank cylinder and letting the compressor run when you aren't necessarily waiting on fills... For a little bit more money though, you can upgrade to a 5-6 CFM compressor which is more reasonable in the air fill speed, filling a tank in 10-12 minutes, give or take...
Size - size seems to be completely dependent on CFM, as there isn't much of a difference in size between comparable CFM electric, gas or diesel compressors...
Chances are, a portable system will be what you want, and you can mount it semi-permanently where it is somewhat out of the way...
