Despite concerns among real estate brokers that the housing market is showing signs of softening, apartment prices across New York City increased by large margins in the third quarter.

According to a market report published earlier today by the Real Estate Board of New York, the average price of an apartment rose 23% to $888,000. Manhattan prices jumped 16% to $1.265 million, while Brooklyn showed the largest price increase of any borough, with a 19% hike to $525,000.

“New York City continues to be the stronghold among the nation’s housing markets,” the president of the Real Estate Board, Steven Spinola, said in a statement. “The strength is not limited to Manhattan, with average prices rising in Queens, The Bronx and Brooklyn as well.”

The picture, however, may not be so clear.

“The third quarter is made up of deals that were negotiated during the second quarter, so it doesn’t take into consideration any fallout from the credit crisis,” chief economist at Halstead Property, Gregory Heym, said. “You won’t see the real impact until the fourth quarter and the first quarter of next year.”

According to the report from REBNY, cooperative apartments, prices were relatively stable in the third quarter compared with the same period last year, increasing just 1% to $633,000. Perhaps most surprising, however, coops in the Bronx surged 11% to $243,000. Condos throughout the five boroughs were also up, reporting a 25% price uptick to $1.097 million.

Manhattan posted the highest price increase, as well as the highest average price, with a 25% jump to $1.455 million. Brooklyn had the second-highest sale price with a 5% increase to $613,000, while Queens had the second highest percentage increase in price of 22% to $453,000.

The the average sales price of housing overall, including condominiums, cooperatives, and one- to three-family homes, was up 20% to $782,000 in the third quarter.