There are a lot of good makers out there, that make a wide range of products. It's hard to say "who makes the best knife" without knowing what properties are important to you. Quality for the price? Overall fit & finish? Hardcore performance? The answers would be different for any of one of those considerations.
Overall, I'd have to say that my favorite three makers RIGHT NOW (this tends to change) are Bark River, Chris Reeve, and Spyderco. There are several other companies that I like, but overall, I guess these are my favorites.
Bark River makes absolutely beautiful, well designed, well finished fixed blades, that actually come with nice sheaths. And the price is about right. They have a HUGE selection of different models and handle options.
Chris Reeve has a very limited product line- but the Sebenza alone is enough to put them in my top 3. The Sebenza is in a league of its own. It's the best folder on the market, period.
Spyderco has an impressive line, their prices are good, and their designs are amazing. Sal and Eric Glesser are two of the best, most prolific knife designers in the world. There is a lot of serious talent and hard work coming from those two, and though they receive a lot of praise for it, I think they deserve more. Their knives dominate the mid-range niche, and deservedly so.
Honorable mention goes to Case, Busse, Ka-Bar, Queen and GEC.