Well, I think it's great that you are trying to be so socially conscious - but the reason you can't find a lot of these websites is because, for the most part, they don't exist.
There are some small, mom and pop operations for party/fiesta supplies. But the only true "party/fiesta supply" story of any note is Partyland. I tried to look-up Partyland but I couldn't find it online. They are located in an area called "Fluvial" and, as far as hotels go, they are close to Holiday Inn. Keep in mind that Partyland really caters more to birthdays (and more specifically kids birthdays) than it does other types of parties, but I have, upon occasion, found a rare great find there.
Custom made papel picado banners - well, we do that! But, if you're looking for another vendor, again, there are several mom and pop places that do things like that, but it's really a matter of walking down the streets and finding someone who does it. If you're going to walk up and down streets for papel picado, I would recommend the Emiliano Zapato area - I've seen pinatas there and, generally, if someone does pinatas, they either do papel picado as well or they know someone who does. You won't find papel picado at PartyLand.
Eco-friendly - I'm not saying it's not possible to find but, to my knowledge, we don't have anyone in Vallarta who carries products like that. The closest you are going to find is Guadalajara - you might try doing a search in Guadalajara and then having them ship it to your hotel/or place where you will be staying.
Small folk art gifts - I can't think of a fair-trade store like what you have in mind. I do know of some stores who sell small folk art gifts, but I doubt the artists are directly getting the proceeds. We do folk art as well, depending on what you are looking for. But, if you are searching for something really specific, honestly my best advice is that you buy artwork from the artists on the Malecon - we used one artist once for wedding favors and he even did specific scenes in specific colors for us and, thus, I know he got all the profit from what we were doing. Or you might also try the Huichol Indians who sell their artwork/jewelry on the malecon - NOT in a store - on the malecon itself.
Socially responsible businesses in the area - I love Mexico (I live here after all!) but socially responsible it mostly isn't. Honestly, most of the most socially responsible people I know are some of the coordinators and the musicians. It all gets rather hazy from there. Mexico has a very strong social-class system and it's generations behind America as far as being socially responsible.
As far as a directory of sorts goes, you might try this board: All Vallarta Message Board for Puerto Vallarta, Mexico - Message Board - Yuku. This is mostly a board for people who live in Vallarta, but it's also for people who come-in every year, etc. I think they have several different directories and you might also try asking them some of these questions - they might be helpful .
I hope that helped somewhat!