So far I haven't been thrilled with the bagel options in JH- my husband and I have almost gotten over our bagel addiction that we developed while living in Astoria (Lot's Bagels, how I miss you!). There's a place on Northern around 90th on the South side of the street that's the best I've found.
I like the bagels at Carollo's Bakery either the plain or the sesame. The bagels at M&V on 86th & 37th are decent but I prefer Carollo's. If I'm in Astoria, I pick up a supply at Brooklyn Bagel & Coffee on Broadway which are outstanding and they freeze well.