One of my favorite shows is NCIS and I was thinking it might be fun to set up a game based around the TV Shows version of NCIS Agents. I'm thinking Savage Worlds could work well for this. What do you guys think?

How about using the Savage Worlds version of Shadowrun to mix it up a bit?

Shadowrun feels a bit too futuristic in my opinion. I mean it's all basically modern times. Some of the stuff Abby pulls off with the forensics and stuff is a bit out there, but for the most part its all real world tech.

GUMSHOE is designed for investigations. Trail of Cthulhu might be too cosmic horror and sanity focused. Bubblegumshoe is designed for teen detectives, but the relationship rules might work well for the slight soap opera undercurrent in the NCIS shows.

I'd be interested in Savage Worlds, maybe something else...

Would the characters be agents at another site? Or would they be an alternate-universe MCRT?

Can I suggest New World of Darkness, the core character sheet. It's simple enough and it will provide you with enough to do anything you want.