I currently attend Gordon-Conwell in Charlotte, NC (extension campus) and absolutely love it. My interests are more academic as well, although the Charlotte campus is definitely more ministry focused. I just happened to live in Charlotte, which is why I am doing the Masters here. I think the South Hamilton campus has more students who are academically driven. If you look at the GCTS staff bios you'll see that a lot of GCTS profs actually went to Gordon in South Hamilton and then went on for further study and came back to teach. Many went to Harvard for phd after their Masters at GCTS. If you go into the masters there with academic/phd pursuits in mind I think it could be a great place for you. They have tracks that are more academic in interest and if you know up front that's what you want to do, you can customize your education towards the end goals you have in mind. Plus, as others have mentioned, GCTS is part of the Boston consortium and you can take classes at Harvard.
As far as finances go, I have several scholarships in Charlotte that make it affordable, but I'm not sure what exists up north.
Good luck!