The first thing you have to do is take a look at his lease and make sure that there isn't any language that would bar an additional person living in the unit. A lot of times, leases have language in them that ask if the tenant would be the only person living in the unit and landlords tend to get bent out of shape when they have someone that resides at the property long enough to not fall under the definition of a guest.
That being said, if the lease doesn't have language preventing an additional person from moving in, your next step (if you haven't done this already) is to sit down with the landlord and prove to them that you are not subletting as you are not a subtenant, but a co-tenant. The way you can go about proving this is if you still maintain a separate residence, receive mail elsewhere, prove who pays the rent (for example, if only your boyfriend pays the rent you cannot be considered a subtenant), prove that there is no lease between you and your boyfriend, etc.
The only issue is if you are there full-time, the landlord will try to make your life impossible as they currently are. Your boyfriend could let her know that she is interfering with the quiet enjoyment of the property.
Here is the applicable statute: It is unlawful for a landlord to restrict occupancy of an apartment to the named tenant in the lease or to that tenant and immediate family. When the lease names only one tenant, that tenant may share the apartment with immediate family, one additional occupant and the occupant’s dependent children, provided that the tenant or the tenant’s spouse occupies the premises as their primary residence.
When the lease names more than one tenant, these tenants may share their apartment with immediate family, and, if one of the tenants named in the lease moves out, that tenant may be replaced with another occupant and the dependent children of the occupant. At least one of the tenants named in the lease or that tenant’s spouse must occupy the shared apartment as a primary residence.
A tenant must inform the landlords of the name of any occupant within 30 days after the occupant has moved into the apartment or within 30 days of a landlord’s request for this information. If the tenant named in the lease moves out, the remaining occupant has no right to continue in occupancy without the landlord’s express consent. Landlords may limit the total number of people living in an apartment to comply with legal overcrowding standards. Real Property Law § 235-f.