Carina, I would probably try what you were thinking re: creating a polygon feature class around the urban/populated areas, whether you do this with a buffer (probably not best) or is you have some other way to designate these areas. depending on the size of you study area, and the population, maybe you can take the roads and buffer those, or take the footprints of the buildings and buffer those. You could assign these polygons a value/weight and then use Polygon to Raster—Help | ArcGIS for Desktop to convert them to a raster for additional analysis.
Depending on the species, paraphrasing what Dan mentioned, suitability even in urban areas will vary, depending on the species. Some species, like moose, which my guess would not normally show as compatible in urban area, actually can thrive (urban like in Alaska, not NYC, but there would other factors there too, of course). I am not a biologist, and no expert on habitat analysis (although we have other staff that are working on that more these days) but have worked with them long enough to pick a few things.
i think the first step, again as Dan was getting at, is to get all your layers/variables/weights figured out, and in matching rasters, then start working with the raster/array math. Remember to keep a copy of the original sets since some steps might overwrite v's making a new raster.
also, although I have note searched, there may be samples of models already posted on the Internet for what you are analyzing. Might be worth doing a few browser searches, unless you intent is to come up with a new method. Don't reinvent the wheel is you don't need to.
