It's a complicated question to answer, and looking at IGF awardees won't settle it, especially since IGF presents only a particular slice of a fairly complex community; further, I'm only looking here at the 2013 slice of the slice. Nonetheless, I was curious if there are any geographical clusters in the list of finalists (I include honorable mentions as "finalists"). This might suggest locations for further investigation; the IGF itself doesn't list any geographical information, making it non-obvious where all these games come from. A few concentrations of activity do seem to be present.
Chicago
The cultural/business center of the American midwest, and home to an indie-game scene I must admit I know almost nothing about, despite having grown up in the Chicago area myself. Indie City Games might be somewhere to find out more. Education-wise, home to the DePaul Game Dev Program and the Northwestern Creative Arts & Technology Studio.
Copenhagen–Malmö
A cross-border region straddling Sweden and Denmark (30 mins by train), though perhaps not quite yet coalesced into a single metropolitan area. Home of the world's largest game jam, and has strong institutional support for independent game production, through initiatives such as the Nordic Game Program, Danish Film Institute, DADIU, and university programs like the one I work in.
Los Angeles area
Long a center of the entertainment industry, and home to a number of big-budget game companies. A number of indie-game studios have come out of USC's Interactive Media Division. In recent years, the main IndieCade event has been held in Culver City.
Montreal
A multilingual English/French city anchoring Quebec's business sector, which includes outposts of large game companies such as Eidos and Ubisoft. A center of independent music as well as games, home to Concordia University's Game Studies and Design program, and benefitting from aggressive game-targeted tax incentives.
San Francisco Bay Area
The center of the technology industry, anchored by Silicon Valley, which includes among its ranks a number of big-budget game companies (Electronic Arts the largest of them). Home to the annual Game Developer's Conference (and the associated IGF), among many other things. Over the hills to the south, one can find the UC Santa Cruz Center for Games and Playable Media.
Seattle–Redmond
A technology industry hub, home to Microsoft, Amazon, and more, including the big-budget Microsoft Game Studios. Also home to the DigiPen game program, the University of Washington Center for Game Science, and community organizations such as Seattle Indies.
Toronto
The biggest center of Canada's business sector, and also home to a large independent game scene, though it might be a stretch to call it "the birthplace of the modern indie movement". For more, Daniel Joseph wrote an in-depth analysis of the community and surrounding factors.
The hubs above (with three or more games each) actually account for fewer than half of the IGF finalists, so indie-game production doesn't seem to be dominated by a few large cities: a lot of activity seems to be scattered throughout the world. I list the rest here, in alphabetical order by city, with some "other" collected at the end.
Angoulême, France: Narcosis and SerpenteS
Austin, TX, USA: Hundreds (distributed team, Austin/Chicago/Vancouver) and The Stanley Parable
Birmingham, England: Renga
Brasília, Brazil: Knights of Pen & Paper
Breda, the Netherlands: ATUM and Farsh
Cambridge, England: Gateways and Super Hexagon
Edinburgh, Scotland: Bad Hotel
Edmonton, AB, Canada: StarForge
Ghent, Belgium: Bientôt l'été
Gothenburg, Sweden: Hotline Miami
Kyoto, Japan: PixelJunk 4am
London, England: Thomas Was Alone
Northfield, MN, USA: Anodyne (distributed team, Northfield/Chicago)
Orlando, FL, USA: Plushy Knight
Pittsburgh, PA, USA: mindful xp volume
Portland, OR, USA: Gone Home
Roubaix, France: FLY'N
Shanghai, China: FTL: Faster Than Light
Singapore: Chrono Disfunglement
Stockholm, Sweden: Eleven
Tempe, AZ, USA: The Bridge (distributed team, Tempe/Redmond)
Troy, NY, USA: Zineth
Utrecht, the Netherlands: SneakSneak
Vancouver, BC, Canada: Hundreds (distributed team, Vancouver/Austin/Chicago) and Pulse
Zürich, Switzerland: LiquidSketch
Other:
There doesn't seem to be an obvious candidate for a hub of indie-game activity not located in a major business/financial center, as Wilson envisions. On the other hand, the hubs don't seem to account for that large a proportion of the total activity, at least the total activity as measured by 2013 IGF finalists. And some major business/financial hubs are absent: London accounted for only one game, and nothing came from NYC, Paris, or Tokyo (though cultural or language barriers may account for the latter). Conclusion: I wouldn't draw any strong conclusions from this information, but it's intriguing.