I don't see there being any reason to mention that this is a rewrite. Agents are going to assume that you have done everything you can to polish up your manuscript, and that might include significant rewrites. If you get The Call, then maybe one of the things they might discuss with you is the genesis of your story and how things evolved, but for your query you have more important things to talk about.
As far as requerying an agent, I think that has to be based on the agent. Some of them might say on their website that you are allowed to requery after significant revisions, but most are probably not interested. If one did reject you but does allow requerying, then that would be the one spot where you might mention that you've made revisions, in particular if they were one who had shown interest before. But this really is a case-by-case issue, I think.
Please note I'm also posting on behalf of people who can't sign up, so if I provide a link in the main body of the post, make sure to reciprocate on that thread.