If your party is evil, then you can really choose either. If you are primarily good, then you wouldn't want to side with evil incarnate would you? Both give you good items in the end, though I think that going vs. Bodhi gives you more XP, and is better for your reputation.
i originally chose bodhi- purely by accident as i was in the graveyard district at night with 15,000 gold. however, the spiel at the start of chapter 3 put me off a bit as it was harping on about making a bad/evil choice so i reloaded and went with the shadow thieves.
When you work with Bodhi you never get the Mace of Disruption. Also you miss Edwin (see "D'oh..." post on this forum). When you work with Aran Linvail you never get the Rifthome(?) Axe. I think the mace is the better choice. That's why I recommend Aran.
What are you talking about Radek? Of course you get the mace just go to the pool and fetch it. And you can get Edwin if you take him in chapter 2. You also get elven chain mail when you finally face Aran.
The Mace of Disruption is actually easier to get: Just walk in and take it. However, you do miss out on Edwin. To get into the building he's in, you need to doing the thief quest. If you do it first, Bohdi won't meet with you. If you meet with her, the thieves won't talk to you.
You can do the Renal quest without joining the thieves (this way you can get Edwin) and after that you can still join Bodhi. (that's what I did the last time I played)