how to make bagels puffier

Bagels are not meant to be "puffy." When that happens, they are just rolls. Bagels are firm and chewy. and they should be boiled before being baked.

I've had great results with this recipe from Peter Reinhart: http://www.latimes.com/style/la-fo-bagelrec12-2008nov12-story.html
An important element is the instant yeast -- the first time I made them I mistakenly used active dry yeast, and they didn't rise as well. I usually use all purpose flour (Whole Foods organic white all purpose) and it works well. I assume by puffy you're referring to the rise, and not a fluffy texture -this recipe makes a great NY style bagel that is both chewy and well risen.

One opinion - if you like puffy, fluffy bagels, probably best solution is to find a bakery or cafe who makes them that way and buy them there..
The large, puffy bagels that we see today developed mid-20c as the bagel moved from small bakeries & delis in places like New York and Montreal to mass-produced and frozen products available cross-country in mainstream groceries.
Early and mid 20th C bagels were generally smaller and denser, and many recipes reflect that. And now some craft bakeries and nouveau delis are returning to making that style.
For a puffier bagel, probably look for a recipe with high ratio of yeast, white flour, long rise and maybe short or no boiling stage.