It will make absolutely no difference. If you boot into Windows, you are only running Windows programs and nothing of data stored on linux-accessible partitions is accessed unless you chose to do so. Accessing data does not slow down the other operating system's functions, so there will be no differnece.
Vice versa is also true if you boot into a linux distribution instead of Windows.
If your machine is slow in either operating system, check your configurations and also check for malware, etc. Also check if your hardware needs upgrading.