IMO
Fighters / bombers; 3000-5000 (latter including cockpit)
Cruisers / Freighter / small non-flyable ships; 3000-6000 (including turrets and destroyed turrets, possibly cockpit / internals for smaller ships)
Destroyers; 5000-8000 (again including turrets)
The turrets thing is sticky.... I have a destroyer with a 3500 poly hull, but the 30 turrets+debris objects makes it 8000 odd. THe other option, of course, is to really simplify the turrets, but then they can become incongrously simple.
Either way, good LODing keeps things playable.
EDIT; for alien fighters - i.e. ones which are likely to be present in higher numbers in a mission for example - I tend to keep a lower polycount (say 1500-3000) and map size. It's partly a matter of the purpose, of course - if you;re working on a campaign, you can modulate the polycount budget based on how many of that ship will be onscreen, and how close you'll get to them.
EDIT2; actually, the highest poly fighter I've made was 4000 (with a very detailed cockpit accounting for a lot of those); the 5000 is an absolute max I've yet to come close to breaching.