Wirelessly posted (BlackBerry8530/5.0.0.601 Profile/MIDP-2.1 Configuration/CLDC-1.1 VendorID/417)
I would never base a taxi or limo tip on the after-tolls amount; only on the base fare. Just like basing a restaurant tip on the pre-tax, not post-tax, amount.
So for a $41 base fare, I would likely tip $7 or $8. If the trip involves crossing a tolled bridge or tunnel, be aware that if the toll is paid with an E-Z Pass transponder -- which will almost always be the case when in a taxi or limo -- the toll charged is less than the posted "cash" toll. For example, at the Queens-Midtown Tunnel, the toll is $4.80 with an E-Z Pass, and $6.50 without. Do not let the driver hit you up for the higher cash toll unless the toll was, in fact, paid in cash.
Here's a link to the toll information:
http://www.mta.info/bandt/html/qmt.html