on 5NL I doubt people bluff, they do make weird plays and you only need 25%. your blocking AQ and AK so he's basically saying he hit a set or 2pair and played it slow. My Advice is you should look at how the population plays, as it's pretty hard for people who don't play the same stake to give you advice about unknown opponents.. it's just really player and population dependent, especially on the micros where nobody has an idea about strategy & just does how they feel like at that time. I wouldn't be surprised if this is a bad call on 5NL, but it could be +EV vs some opponents too. Really no idea how they play.

Personally I'm calling because the guy hasn't bet turn when he has a hand that beats me(set,2pair, straight) and now he's betting river on an offsuit 3. He still has FD's and might turn a hand like QJ into a bluff. Maybe he floated the flop with total garbage like Q9, J9, .. that's why you need population reads:)

I'd bet the river. It seems more likely that villain calls you with a bluffcatcher than bluff or valuebet with worse when you check.

Once you check, it's an easy call, most better hands would've bet the turn already. Villain likely has a hand like AK or KQ.

I think it's better if you bet on the river because he's going to call with some one pair hands that he's going to check back if you check it to him (like QJ, KQ, J9h...)
I guess you will make more money if you bet yourself but I'm not sure