Not sure if it's better with yogurt or not?
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I'm afraid this doesn't really answer your question, but since I see you live in Brooklyn: the best lemon poppyseed muffin I've ever had comes from Smith Canteen, right off the F/G at Carroll Gardens. Maybe they will share their recipe? (And if so, please let me know!)
I like this one from Elise Bauer, which does include yogurt:
It makes a LOT. I usually halve the recipe, except for the lemon zest and poppy seeds, and get seven or eight muffins in a standard tin.
I've had good results with the Cook's Illustrated recipe and it uses yogurt. The muffins are very light. The tops are a little pale, so I want to experiment with darkening them.
I've been looking for a recipe that is similar to the Smith Canteen lemon poppyseed muffins since the place was taken over by strollers and I was then priced out of the neighborhood. After much research (and thinking it must be an oil based muffin, perhaps with buttermilk) I looked on my favorite site, Smitten Kitchen. The closest I could get was the madeline recipe but then I realized that the consistency of the Smith Canteen recipe is similar to a madeline. So. I took the Smitten Kitchen madeline recipe and tweeked it a bit and turned it into a very close version of the Smith Canteen muffins. Mmmmmm. Here's the link to the madeline recipe. Add poppy seeds and lemon juice. You don't have to refrigerate. Then look up a glaze for the top. One tip: double all things lemon! Also, no need to do the yogurt...