Playing their first match in Queens, the defending MLS champions fell behind thanks to an early brace from Jesus Jimenez. After a goal was ruled out, Valentin Castellanos got one back for the hosts before halftime.
The second half saw NYCFC explode with goals from Thiago Andrade, Santiago Rodriguez, Keaton Parks and Gabriel Pereira staking them to a 5-2 lead.
DeAndre Kerr cut it to a two-goal margin and following Alfredo Morales' second yellow, which saw him sent off, Michael Bradley made it a one-goal game before the Boys In Blue saw the match out.
Story of the match
Toronto struck first in the 13th minute as Kosi Thompson and Jonathan Osorio exchanged passes before the ball found its way to Jimenez, who scored off of the base of the post.
After VAR ruled out Castellanos' equalizer three minutes later for offsides, Reds goalkeeper Alex Bono was on hand to deny Santiago Rodriguez.
In the 27th minute, Jimenez doubled his tally and his side's advantage after a fine through ball by Thompson was latched onto by the Spaniard and lifted the ball over Sean Johnson and into the back of the net.
Castellanos cut the deficit in half after being picked out by Andrade, setting the stage for what would be one of the wildest halves of football this season.
Andrade leveled four minutes after halftime as he found himself unmarked at the back post and tapped in a shot by Talles Magno that appeared to be going well off-target.
Rodriguez would give NYCFC the lead for good five minutes later as Alex Callens dispossessed Bradley and Castellanos passed to the Argentine, who finished past Bono.
Parks doubled the hosts' advantage following a broken play in the Toronto box with a low shot past Bono and Pereira seemingly put the match away as his guided shot went through the legs of Chris Mavinga and in.
In the 86th minute, the visitors began mounting a comeback. A corner by Alejandro Pozuelo found the head of Kerr and he rose up to beat Heber and score his first goal in MLS.
The Boys In Blue were reduced to ten men in the 89th minute when Morales was shown a second yellow card. On the ensuing free kick, Pozuelo put a ball into the box that was headed in by Bradley.
Although there was four minutes of stoppage time, nothing came of it and NYCFC moved into seventh place in the Eastern Conference, right above the playoff line.
Man of the match: Valentin Castellanos
He was, as he always seems to be, a threat all afternoon, leading all players with 1.5 xG, nine shots, and four shots on target.