Here's the M90 offerings on that site:
Shapeways 3D printed M90 parts
Those parts are offered in various materials. The smoothest is going to be "smoothest fine detail plastic." "Smooth fine detail plastic" is good too, if price is an issue but according to Shapeways, the "smoothest" should offer the best finish. Regardless which material you choose, you will need to paint them for best appearance. For obvious reasons, it may work out better for you to replace a whole set so they will all match. Otherwise, it is almost certain that one replacement knob will be a different color than the others. If you are a professional painter with color matching equipment, maybe you can get it very close, but for most hobbyists that will spray with a rattle can, it's almost hopeless to get a 100% color match.
As for whether the loose or tree ones, it's up to you. The ones on the tree will require a little more work because you will have to separate the parts from the tree. On the other hand, a "treed" collection might be easier to paint. You can separate after painting but of course the nub that gets cut off will show the native finish. Whether or not a model is offered in a "tree-less" version often varies depending upon how much Shapeways charges. Sometimes, they charge a premium for loose ones, or don't even allow. It all depends on their automated model review process.