I thought the Polo Grounds had an upper deck but maybe it didn't go that far along the third base line?
There is an historic field called the Dyckman Oval which was in Manhattan.
Below is a photo from the tracks with the ballpark on the right in the distance.
This one shows a shadow of the tracks at the right elevation to be riding above the stadium. Unfortunately, I don't think there are any good reference photos of the interior and I cannot find any information on when it was built. But it was used for Negro League games for many years starting in at least 1913. So, possibly earlier and could include your dates.
Just a stab in the dark...
I believe these photos are from much later so that could account for the difference in surrounding buildings? I think the train is a key factor and could help locate the ballpark if this isn't it.