Q: when one gains 5 pounds of lean body mass from weight training are all these five pounds from muscle or does bone mass also contribute to the five pounds?

A: Yup, bone mass and even tendon and ligament mass will increase with weight training as well. That's another benefit of weight training: strengthening bones and connective tissue and preventing osteoporosis. However most of the typical weight gains during weight lifting will be in increased muscle and fat mass.

The increase in fat cannot be avoided altogether for most people when gaining weight (unless using illegal anabolic steroids which I do not recommend), but it can be minimized by gaining weight slowly and maintaining a clean diet. Small fat gains along with muscle gains are not a problem -- you can always switch from muscle-building mode to fat-burning mode by adjusting your diet and burn off the extra fat while keeping most of the newly gained muscle.