I have quite a few bootleg and custom minifigures, and the quality varies. You have to do your homework first. The difference between the two is that bootleg are made start-to-finish by a non-TLG company, whereas customs are official, blank minifigures, printed by a seconary seller.
There are quite a lot of bootleg minifigure producers that operate out of China, most notably Shen Yuan (I think that's what they're called) and Decool (who are dodgy). I have a few of the former - Galactus, Odin, the Thing - but I tend to steer away from characters that TLG actually produces (with my only exception being the Vision). The plastic is noticably different on, say, Galactus, but it isn't by any means bad; if anything, it feels on-par with Mega Bloks. Still not LEGO standard, but not bad either. It's also nice that there is a way to get some characters that TLG hasn't produced yet. I'm planning on getting a few more soon, including a bootleg version of the SDCC Sam Wilson Captain America. If you do your homework, you can normally see whether they're any good or not. My bootleg Spider-Man 2099 looks just as good on camera as a regular TLG minifigure. This thread on Eurobricks is probably a good place to find out more or to get second opinions before buying; a lot of these guys are seriously into it, and have amassed vast collections.
Many, however, are atrocious, so be careful when buying that you don't end up with monstrosities like these.
As for customs, there's a lot of great stuff out there. I'm probably not the best person to ask, since I don't buy many (they're normally upwards of £20) though I did indulge in a Daredevil custom minifigure by poppunkmunky. It's pad printed, the design is exactly as it is in the LEGO Marvel videogame...ye gods, it's glorious. Poppunkmunky also has a Kamala Khan Ms Marvel and a Moon Knight that I want, but again, the pricetag. I only got Daredevil through careful ebay bidding. However, if you have the money to spend, I'd definitely recommend customs. Pheonix Customs (or something of that ilk, I can't remember the name) is also amazing, and dare I say it Solid Brix Studios also produces great work. Brick Ultra's customs are pretty good too, especially the Ultron minifigure.
"Nothing goes down 'less I'm involved. No nuggets. No onion rings. No nothin'. A cheeseburger gets sold in the park, I want in! You got fat while we starved on the streets...now it's my turn!" -Harley Morenstein