Bone in sells for less per lb. because you're paying for the bone! Depending on the the price, and the weight of the bone, it may or may not be cheaper to buy bone in.
In addition, since I don't eat bone, I don't always want the bone in.
As far as boneless chicken breasts, when there's a sale ($1.99/lb) It's a better deal than bone in. In this case not only am I not paying for the bone, I'm also not paying for the weight of the skin, which is the most unhealthy part of chicken.
I don't cut as well as the butcher, so I will often get boneless when the bone isn't needed. A NY Strip does not need a bone. On the otherhand, a T-bone steak wouldn't really be a t-bone steak without the bone.
On the other hand, if I know I have time to make a soup or stock, I'll go ahead and get chicken and/or beef with the bone depending.
So, it all comes down to either whether I intend to use the bone, whether the price with the bone in is really "cheaper" or not, and whether or not I have time to even deal with the bone.
But if you want a NY Strip with the bone, speak to the butcher and ask for it. I'm sure he'll be glad to do it and will adjust the price accordingly.