Service Honda has great prices on Honda parts. They have an ad on the left side of this page. Also check with Mach 1 Motorsports in Vallejo, CA. I have heard the Honda OEM parts are the best.
The entire crank/rod assembly for the CR250 is not very expensive ($170 or so is what I paid for my '99), Crank bearings were about $30 each; a complete gasket set was $70+-. The piston and related top end stuff is around $100 - $120. There are a few small items not included with the gasket set such as the shift shaft seal.
If on disassembly you find your crankcase is damaged beyond repair, Honda does sell individual halfs which already have a crank bearing installed, cost about $170 from Service.