eBay, or use a Craigslist search engine like Search Tempest.
Guessing you'll have better luck on eBay.
Remember that it's possible to use R1150** or K1200RS wheels on your R1100R, given the correct modifications for ABS sensor rings and brake rotors. Board member Oliver (omg1010) from Germany has the expertise on this topic.
Like sweatmark said, ebay would be your best bet. You can use wheels taken off the R850/R1100 R/RS/RT models. The 5-spoke rims of the R1100S/R1150R and K1200 (flying brick) models can also be used but need more or less modification (depending on the rim) and will be a lot more costly ...
The wheels for my BMW R1100R bike were purchased from BMW Motorcycle Accessory for BMW R1100R, they guys that work there are incredible, know every product they sell in and out and are willing to spend time with you figuring out what's best for your application.