I'm not going to make any claims about which position is harder to play. I haven't played organized baseball since little league, and I caught, so I have no clue.
The main factor, though, is the amount of plays at each position. Even if 3rd is slightly tougher, you get more value out of a good fielder at 2nd, by pure volume.
I ran over to BP and did a quick sanity check:
<font class="small">Code:</font><hr /><pre>
AGE YEAR TEAM POS G PO A E DP
MARK ELLIS 30 2007 OAK-A SB 78 147 263 4 55
ERIC CHAVEZ 29 2007 OAK-A TB 79 64 157 6 15
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I just chose the A's because they're the first team that came to mind as having a stable 2nd/3rd combo this season. 3rd base would have to be incredibly tougher than 2nd to overcome this difference in volume.