Why do NY ARTCC Standard Operation Procedures have different altitude limits than the NY Class B airspace?
The commenters have a good point that the SOP documents you liked are for hobbyist simulation and are not necessarily faithful reproductions of real-world procedures. But even in the real world who owns which specific volume of the air at which specific altitudes is not necessarily correlated with the regulatory airspace class for a given volume of air at a given altitude.
The two altitude limits are different (not &quot;incompatible&quot;!):

One is regulatory, and binding on pilots. No pilot may operate in the Class B airspace, unless they have received a clearance from ATC allowing them to do so. For IFR aircraft, they will receive their clearance on the ground; they will be cleared to fly a certain route at a certain altitude, and it does not matter what airspace class the route crosses or enters, because they have already received a clearance to fly that route. For VFR pilots, they may operate as they wish in Class E airspace, but before entering Class B airspace must receive a clearance from ATC telling them which heading to fly at what altitude. (There are similar but less restrictive requirements that VFR aircraft must abide by to enter Class C or Class D airspace.)
The other is not regulatory, and has to do with ATC. Regardless of the airspace classification of any volume of air, one and only one specific control position is responsible for all aircraft operating within that volume. The document you found lays out the boundaries (in 3D space) for those volumes of air, which are not directly relevant or known to pilots. The volumes will be designed so that certain activities (arrivals joining the localizer and coming in to land, or departures climbing away from the airport) can be monitored and controlled by only one controller without unnecessary handoffs.