Plane owners scored a new tax break on fuel. New York City’s long-gestating Second Avenue subway got nearly $1 billion. And both teachers unions and charter schools applauded the funding they received.

But New York’s $147.2 billion state budget, approved by the Legislature late Thursday, faced criticism for its spending levels and how it came together.

Overall, the budget, which applies to the fiscal year beginning April 1 and ending March 31, 2017, was up from last year’s $142 billion. Its biggest expenditures, similar to many state budgets, have long included Medicaid and public education.

Negotiations in recent weeks were overshadowed by Gov. Andrew Cuomo’s push to raise the minimum wage and implement a paid-family-leave plan, issues that drew national attention, but other contentious measures were sorted out as well.

School aid for prekindergarten through 12th grade was boosted $1.5 billion to $24.8 billion, a 6.5% increase from last year. New York’s $19,818 average cost per student is the highest in the U.S. While that still fell short of the numbers some education advocates called for, teachers-union leaders praised the budget’s elimination of the “gap-elimination adjustment,” a postrecession formula for cuts to school aid.

“New York is making strides,” said Michael Mulgrew, president of the United Federation of Teachers, who in the past has been one of Mr. Cuomo’s biggest critics.

Charter schools, which have the strong support of Mr. Cuomo and the Republican-led Senate, also saw funding gains. The budget also defeated a proposal pushed by Assembly Democrats and teachers unions to toughen laws requiring that charters serve more hard-to-teach students.

Statewide infrastructure and transportation spending rose to more than $55 billion. A slice of it, $950 million, is marked for extending the Second Avenue subway to East Harlem, fueling optimism for the long-stalled Manhattan project.

“It’s been postponed so many times,” said Peter Derrick, a transit historian who is co-writing a book about it. Thursday’s budget deal, he said, “keeps the momentum going.”

Among those disappointed in the budget were HIV/AIDS activists. Mr. Cuomo in 2014 announced a plan to bring AIDS below epidemic levels by 2020, but health advocates said this year’s budget was shy of the $70 million they requested.

“For the AIDS community, the budget is a historic failure,” saidJeremy Saunders, co-executive director of activist group VOCAL-NY.

Officials at the State University of New York also said they were disappointed in the budget, because it ended a plan of gradual tuition increases and according to them, didn’t provide necessary resources.

At the City University of New York, there were mixed feelings. While CUNY fended off a feared state spending cut, the budget didn’t address the requests for new faculty contracts, which expired in 2010.

“We will not stop demanding economic justice,” said Barbara Bowen,head of the school system’s union for faculty members.

State lawmakers on Friday, many of whom hadn’t slept, criticized the budget for procedural reasons.

They didn’t see the details of the spending plan until late Thursday and had to vote on it almost immediately, without the chance to closely read thousands of pages in policy language.

The Citizens Budget Commission, a government watchdog group, questioned Mr. Cuomo’s calculations, saying that “given the lack of transparency in the process, it is unclear how the State is limiting” growth.

E.J. McMahon, director of the conservative think tank Empire Center for Public Policy, criticized the budget for pledging millions in discretionary funds, something he called “one of the many deals reached behind closed doors.”

An odd nugget tucked into the budget also turned some heads: the exemption of a local sales tax for airplanes.

Some liberal lawmakers questioned if it was there to benefit New York’s wealthy private-plane owners, but Mr. Cuomo’s office said it was part of a tax restructuring approved by local counties as part of a federal mandate to spend aviation fuel tax on airports, or eliminate them altogether.

© 2016 Wall Street Journal