Am I allowed to charge more for an apartment if the tenant is a voucher user versus regular tenants?  

Like for example, there are huge penalties in the city with regards to security deposits that have led to landlords taking non-refundable move-in fees instead of security deposits.Lastly, since it appears that this is your first rental property, please know that as of fairly recently, in Cook County landlords can no longer discriminate against Section 8 aka housing voucher tenants.

I attained the holy grail of a Section 8 voucher last year, which was accepted at the subsidized apartment I was already in.  

That is related to public housing, which is different than a private landlord renting to someone with a section 8 voucher. 

There are some parts in Brooklyn where a 3BR would rent for double that and other places where a 3BR would go for $1,500.Being that Section 8 will give the tenant a voucher for $2,021 why doesn't every 3BR in NYC rent for $2,021 regardless of location?

Finally, the subsidized housing vouchers require a year lease and not a month to month.  

This town even keeps an open Section 8 list, and there is high turnover even in subsidized housing with Section 8 tenants - something you don't see most places, because it's so hard to get and keep Section 8 vouchers.  

this is not okay, you can lose your voucher and landlord risk being on a list. 

No, the ordinance is talking about Section 8 vouchers regarding the 3X rule.  

Once a tenant has rented for a year without problems, HUD then allows them to rent a place that is more rent than they are approved for on their voucher.