Fascinating place, with an incredible history. I recommend going with a guide (Augusto from Andes Tours (located in Hotel Revash) speaks very good english and gives good information, the cost is 45 soles (guide and transport only), although you might be able to negotiate). Cheaper tours are available, but the guides may not be as good. The problem with going with a tour however, is that you won't have time to yourself, and in a place like this, having time to sit down and just soak it in is really important (I regret this!). So perhaps negotiate a cheaper price and find your own way back afterwards.
Entrance is currently 15 Soles, cheaper for students. You can now drive almost to the ruins, with only a 15-20 minute walk. This is perhaps a bit disappointing, as the old trek probably added to the experience and prevented the more annoying tourists from visiting! You can also stay in the local village of Maria or camp and this would enable you to come up early in the morning and miss the (not huge) crowds. There is a restaurant in Maria that does good grilled trucha, but I can't remember the name (it's on the left as you come up into Maria towards Kuelap and it pretty big so should be obvious).