Is it customary to pay to the Seller an amount equal to one and one-half percent (1.50%) of the sale price of the Unit as a fee to Seller for Seller filing for partial tax exemption benefits pursuant to Section 412-a?

No. Cross it out. Indeed the seller can ask for anything - even to pay his cab fare to get to closing - it does not mean you have to agree. Asking extra 1,5% - is a red flag. Make sure there are no other junk fees in your contract.

It's customary in NYC to pay a $500-$1500 fee for the filing of the tax abatement application. In fact, you don't pay it, you reimburse the seller for the money he spent on this application long ago, before he started construction. I suggest you agree to that - it's your tax abatement after all... Before you reimburse the seller for filing for tax abatement - request proof that he actually did that and have your attorney verify the paperwork provided by the seller. I was not aware there still is tax abatement in Manhattan...

What a momentus subject line.

Yeah, Igor's right, cross it out. Maybe replace it with a provision where he pays for you to get a massage after the closing. Make sure it includes the tip.

Thanks for your input. The new condo development is in the Bx; asking price $200K.

My advice: tell the seller you agree to pay $500 and you WILL NOT verify how much he actually spent. Settle for not more than $600-700. If he still wants you to pay more than that - request proof of his expenses.
Sellers rarely do processing of TA applications themselves. They usually hire expeditiors - and the reimbursment they expect to get from the buyer depends on how expensive that particular expeditor was.
No expeditor charges $3000 for one application, that's for sure.