My question is given that the content of my tab pages are separate aspx pages, should I go with JQuery tabs or tabs control from the ajax toolkit
Given that, AjaxControltoolkit isn't really an option. AjaxControlToolkit tabs are controls, which means they need to live inside a server side form. Even if you could get them to load the contents of another ASPX page, the most likely result of that would be nested html forms, which isn't really supported.
If you go the jQuery UI tabs route, you will most likely run into different issues:
page redirects on postback. You could try to work around that problem using the jQuery Form (something along these lines), but you might have a hard time working around controls that submit forms using the __doPostBack method. If your ASPX pages rely on postbacks, your best bet is probably to host an iframe for each tab and load your aspx pages that way. That will allow your pages to still function properly with postbacks.
ASP.NET MVC lands itself much better to the setup you're trying to achieve if that's at all an option.