Here is the website for the Mannahatta Project. You can find what animals and other species probably lived in Manhattan in 1609.
Prodigal Summer, By Barbara Kingsolver, is a novel which explores topics in ecology. ISBN: 0060199652
Overview of what urban ecology is and some considerations that are required when thinking about an urban ecosystem:
Here is a series of videos about urban ecosystems and the wildlife's interactions with these ecosystems. These videos focus particularly about the adaption of animals and other species to living in an urban environment. I recommend "Unwanted guests", especially, for thinking about the current role these animals play in the changing urban ecosystem.
This is a website all about population growth. (Note the very first part is not as relevant)
This has information on interactions within the ecosystem.
Information about food chains and the transfer of energy within an ecosystem.
This site gives a specific example and explanation of a predator prey relationship.