What are the mechanics for an infiltrator successfully taking over an enemy unit? Is it a random chance? I've got an infiltrator right next to a bunch of derelict alien boats, but can't for the life of me take them over. What do I need to do?

AFAIK, it depends on their veterancy. For each successful disable/steal, the infiltrator has a chance of raising its level (represented by various ranks and a +X under their name). The higher the rank the better the chance. You can see this % chance of success graphically before you take action, it is represented in the cursor. If you are trying to use a rookie to take over a derlict, it will take quite some time. I did this last night, but it took about 8-9 turns before the infiltrator succeeded. Typically, disable is easier than steal, so If I have time, I try and build up my infiltrators by continuously disabling something a few turns before stealing it.

Yeah, I tried mapping this once and noticed a few things.
Namely, the % chance of stealing something seems to vary from unit to unit .. in other words, its much easier to steal a Fuel truck than it is an alien aircraft ...
Things that make it easier: disable them first (*duh*) ... and have multiple infiltrators ...
as for getting those alien derelicts .. just keep working at it ... since it is random, I've played games where I've walked right up to an alien aircraft and nabbed it first try .. other games, 20+ turns with 10+ infiltrators failing to capture a single alien tank .. *sigh*
In all honesty, I love MAX, but it's the one thing that irritates me about the game .. think about it .. their tag-line for the game is, essentially: "Hey look, no randomness, it's just like chess!! You have to use strategy, not just flail about and hope to get lucky!" .. but then enter the infiltrators ... *huh* ? I've always been confused why they were random ... nice idea, poorly executed .. (not that I have any better ideas off the top of my head .. :) hehe)