Winer was born on August 31, 1800 in Durham, Green County, New York, although he was educated primarily in Auburn, New York. His mother was English and his father was Dr. Andrew Winer of Germanic descent. Dr. Winer had been a doctor with the King’s forces during the Revolutionary War and was a well-known physician in his time. He moved to the Niagara district in 1821. He began as a blacksmith in Jordan, a town half way between St. Catharines and Hamilton. Soon after, he became a student of the Thompsonian system of medicine. This system involved concoctions of roots, vegetables and other household edibles. It was very popular at the time as a cure-all brand of medicine. The demand for Winer’s "potions" increased and he soon gave up the blacksmith profession entirely. He moved to Hamilton in 1829 and a year later he opened his own business on the northeast corner of King and John Street.

In Hamilton, Winer was known for his "public spirited efforts." For the eight years preceding the city’s charter, Winer was chairman of the Board of Police, which was the governing body at the time. He was also one of Hamilton’s pioneer alderman, representing a ward on city council for many years.

When Winer came to the town of Hamilton, most of the land was farming property. There were only two other stores and one tavern; they all did little business. There certainly were not any other druggists in Hamilton at the time. Winer advertised the opening of his store in a half-column newspaper article, asking people to come see the "large and elegant assortment of drugs, medicines, paints, dye-woods and dye stuffs." But not long after opening the store, Winer changed his inventory to include only drugs. Over the next 54 years that Winer remained in business, he made himself a large fortune. Every man in his employ became rich and independent as well. This was quite a feat, since all other local business of that time "either failed, died or sold out."

There were a few glitches in Winer’s business though. He was once involved in a legal dispute with a New York druggist named John Moffat. Moffat claimed to have patented "Life Pills" and "Phoenix Bitters" and accused Winer of counterfeiting them. Moffat claimed that Winer had forged his engraved signature on the pill labels and offered to sell them to other druggists at a lower cost. After Moffat’s lawyer apparently asked Winer to stop the counterfeiting, and Winer refused, Moffat began to slander Winer in his local newspaper, "The Good Samaritan." In retaliation, Winer started his own paper, "The Bee", in which he described Moffat as a "vile morsel of mortality," a "filthy mass of rubbish," an "unblushing quack," and referred to him as the "New York reptile." After a brief war of words, the counterfeit claims were dropped and the event more or less blew-over. Another unfortunate occurrence happened in 1845 when the Winer firm was devastated by a fire. Most of the business was completely destroyed. However, Winer rebuilt quickly and was seemingly undaunted by such a tragedy. He did require some assistance, however. In 1848, C.N. Sims of Montreal entered a partnership and the firm became known as Winer & Sims. In 1853, Lyman Moore entered the partnership and the firm was called Winer, Moore & Co. George Rutherford joined in 1858.

By 1862 it was clear that Winer’s business had recovered from the damages done by legal disputes and a fire. The firm discontinued the retail department in favour of supplying the country with wholesale drugs.  In 1863, they started a glass manufactory, Hamilton Glass Works, which became an important branch of their business. In 1876, Winer became president of the Canada Fire and Marine Insurance Company.

In 1882, Winer suffered from a stroke and his health took a drastic turn for the worse. He retired as head of the firm in 1883, stepping down from the company he had been senior member of for 54 years. John Winer died on August 1, 1887 and his obituary read that Hamilton had lost a great citizen.