His teammates, meanwhile, swung away -- and connected.
Niese (4-4), who has been plagued by a lack of offensive help this year, won for the first time since May 22 and enjoyed pitching with a big lead.
"It was a good feeling," he said. "We hit them hard and hit them early. It's a lot more comfortable going out there, and you're able to pound the zone."
Niese allowed less than four earned runs for the 19th consecutive start, giving up three in six innings.
"The offense really busted out, and Jonathon did another great job," teammate David Wright said. "Every time he takes the ball, you think he's going to go nine innings, and offensively we haven't done a lot to pick him up. I'm glad we were able to do that today."
Niese -- batting eighth -- drove in a run with a bunt in the second inning. Manager Terry Collins joked that he hadn't called for a suicide squeeze since 2006, and Niese said it might have been the first of his career.
"Luckily was able to get a pitch I could put down," Niese said.
Kirk Nieuwenhuis scored without a play for a 2-0 lead.
"The squeeze was huge," Collins said. "We don't do that much, but I wanted to see if we could get something started, so we tried something different."
The bulk of the offense, however, came from higher in the order. Wright drove in a run for the sixth game in a row. Curtis Granderson thrived again in the leadoff spot, reaching base four consecutive times. He and Lucas Duda each had three hits.
Murphy had two hits, including his sixth homer. Nieuwenhuis, making his first start since being recalled from Triple-A, doubled twice.
"We've been waiting a long time to break one open," Collins said. "People think we play ugly game. We're getting beat 4-3 and 3-2. We're hanging in there. We get a lot of guys on, we just haven't been able to get big hits. When you have big hits, you look great."
Rookie Anthony DeSclafani (1-2), making his fourth major league start, gave up seven runs in 3 2-3 innings and departed with a 7.59 ERA. He was unable to keep the ball down or throw breaking pitches for strikes.
"I fell behind hitters, and the fastballs were flying up in the zone," he said. "When that happens, you're not going to get the results you want."
The Marlins (37-38) fell below .500 for the first time since April 30. Ten days ago they had the best home record in the majors, but they went 3-7 on their longest homestand of the year, losing all three series.
"You just have to keeping grinding and stay positive," Garrett Jones said. "It's a long season. Every team runs into this type of thing where the offense isn't clicking and the pitching isn't clicking."
The Mets had scored a total of 13 runs in Niese's previous five starts, but he led 7-0 before giving up three runs in the sixth. The left-hander then struck out Derek Dietrich with the bases loaded to end the inning and his afternoon.
Niese's performance was part of a trend. Mets starters have an ERA of 1.74 over the past six games.
The Mets have won four of their past five, but they still trail NL East leader Washington by five games.
"If we keep the starting pitching going and keep the offense going, I think we should climb back in this thing," Niese said.