It really depends on what part of the system you are on and where the train tunnels are.
The deepest grades are when a train runs under the East River between Manhattan and Queens or Manhattan and Brooklyn. The reason why the river tunnels have steeper grades is that part of the tunnel (usually right in the middle of the river) actually sits on the river bed for support. So, depending on how deep the river bed is, and how deep or above ground the stations are that are right next to where the tubes are under the East River, that will affect the grade.
The steepest grade for a train that goes under the East River is where the N,R and W go through the 60th st. tunnels. The tunnel runs between the Queens Plaza station and the 60th St/Lex. Ave. station.
On the Queens side, the N and W platform at Queens Plaza is an elevated station. When a train leaves there, it has go go from the height of the station down to the river bed level and then back up to the level of the Lex. Avenue station. Believe me, if you ride on an N or W train from Queens Plaza going to Lex. Ave, you will see how steep the grade is and how fast the train will go. Back in the days of when the Brightliners (A.K.A. the R-32's), the R-40 slants, the R-40 modified and the R-42's ran on the N and W, and an N or W train was not stuck waiting for an R train to cross over, the train could easily accel from 0 to at least 60 M.P.H. The fastest ride I've had in that tunnel is on an N train that went up to 68 M.P.H. in the 60th st. tunnels.
Besides the tunnels that go under water, the tunnels under land can have gradients as well, but they are slight. For instance, there are stations where you have one set of platforms on top of another set of platforms, such as the 59th st/ Columbus Circle, West 4th st. Bergen St. 5th Avenue (on the E/V) and 7th Avenue on the B,D,E, a train will have to go up a gradient or go down a gradient to get to that station.
Then, if a line's tunnel has to go above or below another line's tunnel, there will be a gradient for that (for example, the B/D express tracks that are between 34th St/Herald Square and West 4th St. run under the Path tracks and under the 14th st. L line.
Then, there is topography, but usually tunnels under land won't have too steep of a grade to deal with topography.
Above ground lines also have gradients, depending on topography, and if one above ground station is above another above ground station (for example, the L platform at Broadway Junction is over the J/Z platform). Also, between each station, when the train leaves, it goes down a slight gradient to help the train accelerate, and when it gets near the next station, there is a slight upgrade that helps the train to slow down. When you ever go on an elevated line, you will notice that.
Open cut lines also have slight grades (such as the B/Q run) will have grades, but then that depends on the topography of the land.
The other grades that are around are when a train runs from an underground station to an above ground station, such as when the 7 runs between 45th Road/Court House Square and Vernon/Jackson.