It marked the 700th home run collectively for the Griffey family. It was also his 548th career homer, which tied him with Hall of Famer Mike Schmidt for 11th on the all-time list.
It also helped the Reds shake a miserable 2-8 homestand, and the win came against the team with the National League's best record.
"It's a lot of fun to be a part of," Griffey said.
Ken Griffey Sr. had 152 homers during his career. Only Bobby and Barry Bonds (1,050 homers) have combined to clear the fences more often as a family.
Griffey Sr. was among the 41,874 spectators in attendance at Shea Stadium.
"I'll give it to him. He'll get it," Griffey Jr. said of the ball that was retrieved by ballpark security. "Even though it's one day late from Father's Day, so I don't have to give him a gift."
Which milestone number meant more, 700 or 548?
"700 with my Dad," said Griffey, who admitted he had been pressing to get the homer at Great American Ball Park.
"For like the last week," Griffey said laughing. "I was a little impatient with certain things. I hit 500 on the road (in St. Louis in 2004). I just haven't been able to hit one at home. First game on the road, I hit it. I wanted to do it at home to give our fans something to cheer about. It didn't work out."
Cincinnati stepped up with 12 hits, the most since collecting 10 on June 8 against the Cubs. In the previous nine games since, the club batted .217 -- including a .198 mark while being swept three-straight over the weekend by the White Sox.
June 8 was also the last time a Reds starting pitcher found his name in the win column. Just like on Monday, the winning pitcher was named Arroyo. The right-hander scattered two earned runs and seven hits in his second complete game of the season.
"We needed that bad," said Arroyo, who walked one and struck out five. "The bullpen has been run down a little bit."
Arroyo began the game by allowing a leadoff double to Jose Reyes, who later scored on a groundout that gave the Mets a 1-0 lead. David Ross' RBI hit in the top of the second evened the score.
Hernandez (4-6) kept Arroyo and the Reds close and gave up two runs over seven well-pitched innings.
"[Former Red Sox teammate Kevin] Millar used to call me the poor man's El Duque," Arroyo said. "We throw a lot of breaking balls, change speeds, change angles. We're very similar."
Following Griffey's homer that put him ahead, Arroyo's performance really stood out from Hernandez's. He retired eight of the next nine batters he faced.
"Today was one of those games where I didn't have a great read on any of their hitters," said Arroyo, who is 9-3 with a 2.47 ERA in 15 starts this season. "Fortunately, I threw some pitches and I thought they'd just missed and they popped up or hit some weak fly balls."
Brandon Phillips' bases-loaded double in the eighth off Chad Bradford scored two runs and gave Arroyo breathing room. Taking his three-run lead into the ninth, he had no intention of yielding to the bullpen -- which has a 5.01 ERA and is enduring some of its worst struggles of the season.
"I didn't really have any hard innings on my arm or body," Arroyo said. "Even innings where I threw a lot of pitches, I took a lot off and threw a lot of changeups. None of them really took its toll on me."
New York kept it tense when Carlos Beltran smacked a ninth-inning leadoff homer to right field. A one-out single by David Wright brought the tying run to the plate. The Reds' bullpen remained idle but Reds manager Jerry Narron wasn't thinking "Arroyo or bust."
"I wasn't going to put him in a position to lose that game as well as he was throwing," Narron said of his starter. "No matter what the results we've had over the last couple of weeks with our bullpen, I'm still not afraid to use those guys."
Not shaken by the late adversity, Arroyo attacked hitters to the very end. With his 116th pitch, he got Xavier Nady to ground into a game-ending fielder's choice play at third base.
"He is a tremendous competitor," Narron said. "He is fearless and one of the best pitchers in baseball. He's got a great feel for what he's doing out there. He knows how to set up hitters. It's a lot of fun to watch. I love to see guys on the mound that know what they're doing. Sometimes you think it's a lost art for guys who can pitch. He's one of those guys that can still do it.