If it's between those two, I would recommend the e39. The e60 535 had a slew of high pressure fuel pump (HPFP) issues, which is actually how I ended up with a 550 instead.
See threads like this for details:
http://5series.net/forums/e60-discus...roblems-99815/
Obviously, as with any older BMW, be prepared for maintenance items that could get costly. But if you're smart about you it will be well rewarded.