Translator here! And... yeah, it does seem that Nagisa is a boy (I thought he was a girl at first too, honestly). He uses the male pronoun "boku" and other characters refer to him with the suffix -kun. Granted, -kun can be used for both genders, and tomboys in manga are known to use "boku", but Nagisa is definitely not the tomboy type. Oh, and he wears the boys' uniform (though that's hardly good proof, since uniform swaps seem pretty common in manga).
I did find it a little strange that no one uses any pronoun words for Nagisa, but always refer to him by name (Nagisa or Nagisa-kun). I know it's very common to do that in Japanese, but there was one panel in particular that I translated as "Terasaka-kun and the others held no regard for Nagisa-kun's welfare" where the original Japanese looked like this: 寺坂君達は渚君を渚君は自分を大切にしなかった (terasaka-kun tachi ha nagisa-kun wo nagisa-kun ha jibun wo taisetsu ni shinakatta). As you can see, Korosensei uses Nagisa's name twice in the same sentence, rather than replacing one of them with a pronoun instead.