Leaving aside the question of "best," and leaving aside that poll I linked to earlier, I'd like to meditate for a moment on the nature of what characterizes a good beer town.
Beer is local. In the middle ages, every town had two buildings that rose higher than a story--a church and a brewery. Breweries depended on local agriculture and water for ingredients, and these limitations created the distinct styles we now celebrate. In the modern era of globalism, breweries are no longer restricted; a good brewer will have traveled the globe and tried hundreds or thousands of foreign beers, all of which inform his own styles. But even with globalization, beer is local. We have other limitations. The beer you'd wish to drink in the heat of Phoenix, the gloom of Oregon, or the elevation of Santa Fe differs. Our regional and ethnic history contributes to the styles we admire. Finally, local ingredients, even in the age of globalism, can definitely play a role in creating regional styles.
So a city should have a unique beer culture if it's a "beer town." I've got or have had relatives scattered across the Mountain West, and while cities like Boise and Salt Lake have local brewpubs, they're as generic as Applebee's. These are not good beer cities, however good an individual brewery may be. Ask yourself--what's an "Idaho beer?"
A good beer town should have not only the ready availability of distinct, local beer, but a public clamoring for it. I like to check out little Mom and Pop grocery stores to see what beer they stock. In a beer town, they will have a decent selection of micros and imports. I look at the taps in hole-in-the-wall bars and also upscale bars. In a beer town, they'll both have some decent selections. I look to see whether there are regular local beer events--festivals, tastings, brewing dinners, meet-the-brewer events, that kind of thing. You only have those events if the public is demanding them. Are there taprooms in the city that feature a slate of a dozen or more exceptional taps? How many of these places are there? Have some of the local upscale restaurants, influenced by the brewing scene, begun to feature beer along with wine? Here's an especially potent test to run. If I go to a city, can I find any place with a Belgian beer on tap (Stella excepted)? A city can't call itself a beer town if the answer's no.
Looking for the "best" beer town is a fool's errand. Portland, a city of a half million, is clearly the most saturated environment for beer. That's in large part a function of it being the right size--too much smaller and it wouldn't have a critical mass to support all the activities, and too much larger and you'd find a population with more varied interests. Surely there are as many good places to get a pint in San Francisco but, owing to its size, the level of saturation is necessarily less. We can't identify a "best" because it's never going to be an apples-to-apples comparison.
It is possible to identify "good," though. I'd look at some of these indicators I've mentioned. Strip away local boosterism, and there are sadly fewer good beer cities in the country than we'd like. Fortunately, the number is getting larger by the decade, not smaller.