My plan for most of the money is to invest it for retirement in stocks and bond funds.  

We saved up money and now have the money to buy the house.

If you are planning on exiting the property within a short amount of time the benefits may not be worth it- I would check with your CPA and/or cost seg tax specialist on it- Michael Blank interviewed a cost segregation expert on his show- episode 23 I believe titled "Save BIG with Cost Segregation for Multifamily Buildings"- they discussed cost segregation on SF + multifamily assets so I recommend checking it out!

After reading I don't know how many books on investing and financial independence I decided real estate was the answer.My life's goal is to retire while I am young enough to appreciate my retirement.

The reason you see agents driving new cars and wearing bling is because the majority of them have already retired from a previous career or are married to someone providing a steady paycheck.I have 160 agents in my market.

I had been holding on to this money for a couple of years hoping to get a multifamily , but the prices in NYC are just crazy right now, I feel that we're in a bit of a bubble, and it came down to a choice between keeping it in a 1 year CD and generating 4K,or paying off my mortgage and saving 8K/year.

Should i look to investors/ loan/ line of credit and borrow money or wait like a year and save up?

Is it out of your job, vacation fund, retirement money added to a 401k, taking care of aging parents....You determine what the goal is and the answer will become crystal clear. 

With either structure, it's generally recommended that you do not commingle retirement and non-retirement assets.

Unless you are doing good volume it likely is not going to save you much.