Are there any frequent guest programs for independent or boutique hotels?

I travel a lot for work and am burned out on the Marriott-Hilton-Hyatt scene. I have recently started seeking out mid-scale and upscale boutique hotels (like the Algonquin in NYC or the Metropolitan in Toronto) and I really enjoy the character you get at places like those. But I miss my free nights. Is there a network or frequent traveller program that focuses on smaller, boutique hotels? I know some or most of the smaller chains have their own programs; I'm looking for a program that gives me a lot of variety/choices in hotels and still allows me to get rewards.

I travel primarily in the US with about 3 trips a year to Canada; mainly on the East Coast but some West Coast travel; hotels themselves should be priced similar to an area Marriott/Courtyard/Hilton/Embassy Suites or else work won't pay.

Thanks in advance!