Senior center Matt Klinewski scored 20 with 12 rebounds, and senior guard Alex Barr added 15 points for No. 7 Eastern (9-2, 2-1).
"We didn't shoot well," Eastern coach Joe Murphy said. "They did a good job of collapsing down on Matt, and we had some open looks that we missed."
Cunha found himself in a center of a celebration when the final buzzer sounded and Cherry Hill East's student section, the "Cougar Countrymen," charged the court.
"It's like no other feeling," Cunha said. "The fans here are the best. It's so much fun to play in these games."
Cunha spent his first three years at Holy Cross. He transferred to Cherry Hill East for family reasons.
"Everybody made me feel welcome," Cunha said. "Basketball helped with the transition. I knew a lot of the basketball players, but I really didn't know anybody else" in the school.
Cunha, a 5-foot-10 lefthander, had been a steady starter through the first 11 games. But he made a major impact in this battle of fierce rivals, sinking four three-point jumpers.
"I haven't been shooting well, but my teammates have been telling me to keep shooting," Cunha said.
Behind Klinewski and Barr, who scored 10 in the fourth quarter, Eastern took a 50-45 lead with a little more than three minutes left. Wetzler rallied East with a pair of three-pointers, the second giving the Cougars a 51-50 lead with 1 minute, 35 seconds on the clock.
Silpe stretched the advantage to 53-50 with a pair of free throws with 35 seconds remaining.
Barr cut the lead to 53-52 with a basket off a drive, and East missed the front end of a one-and-one. But sophomore Tim Perry blocked a shot, and Cunha grabbed the rebound and was fouled with 11 seconds left.
"I just told myself to take deep breaths, and I knew I could make them," Cunha said.
Cunha made both free throws for a 55-52 lead.
After an Eastern miss, East's Josh Brown added a free throw with three ticks on the clock. Eastern scored at the buzzer.
"This is a great win for us," Cunha said. "We hadn't practiced in two days [because of the snow], and we knew they were a great team. We played together and pulled it out."
Eastern 6 22 9 17 – 54
Cherry Hill East 7 21 12 16 – 56
E: Matt Klinewski 20, Maliq Sanders 9, Alex Barr 15, Tom Flacco 5, John Scalindro 2, Justin Fendrick 3.
CHE: Jake Silpe 13, Austin Wetzler 18, Tim Perry 4, Phil Cunha 16, Tommy Smierciak 4, Josh Brown 1.