BAF missions in Dundee against the Kusari are paying between 500 and 990k, but the pilots are only worth 1500 creds.
The IMG Missions in Tau 23(?) from Falkland Base are paying around 500k, plus the Outcast Pilots.
Missions in Omega 49 and 50 against Corsairs are paying up to 990k as well, when your hold is full with 'sairs, go to BPA Newgate and sell them for 17500 credits a piece:D
All missions are vs. fighters only, be careful with anti-Molly missions from the BAF though, they tend to spam Gunboats.
There are some rather ... incredible ... missions against Corsairs (I know, heresy that anyone would consider killing Corsairs... :P) available at Rostock in Omega-15.
Sure, the mission pays right at 950K, but on an assassination mission, having to go up against a total of SIX Osiris' is definitely more than one ship can handle. Actually, the last time we did one of these, it ended up with 6 of us - 3 bombers, 2 gunboats, and a battlecruiser - and fortunately going up against NPC's, re-engaging is NOT against the rules. (We kept one guy in range while the other people that got blown up either got new ships, or in the case of my battlecruiser, ran off, got more bots/bats/repairs, and then came back.) But we also ended up getting more than 8 million worth of credit cards, pilots, gear, and payment for that mission... :)