I have Logic Pro running on MAC, and I have huge memory on my Windows desktop to run Kontakt as sampler, does RTP MIDI is the best way to connect between them?
you'll want to find something that allows you to run MTC over IP. I am fairly sure there is a feature built into OSX that allows you to route MTC over IP but as for receiving it on a windows platform - that I am not sure of. Certainly look for MTC over IP tools and software - that's where your answer lies.
Update: Checked out RTPMidi - looks like that might be a very good place to start.