Check out
www.supercrewsound.com for sub boxes. They are pricey, but they're good. You can also look into some behind-the-seat boxes in a double cab.
You're going to have to decide what budget you're working with and what kind of sound you're looking for. As long as the amp is matched to the speakers in power rating, you're going to get pretty good quality. Stick with speaker brands you've heard of, and my advice on amps is to go to
www.crutchfield.com and find an amp you like, then go buy it on ebay.