Evan,
Are you referring to the opening port-lights or the fixed port-lights? Possibly the simplest/cheapest long term fix for the non-opening port-light is bolting plexi/laxan/polly on the outside of the hull. This is not a beautiful solution however. If your leaking issue is just in the bedding compound between the port-light and the boat then the solution is relatively straightforward, just remove and re-bed. Mine were leaking where the frame joint ends came together, which required some monkeying around. they could also be leaking between the glass and the metal frame I guess, in which case I have no ideas about repair. =[
If you mean the opening port-lights, I think some of the aforementioned solutions may apply. or check into replacing with new ones. I have heard good things about new found metals.
Good luck.