My honest opinion is that HOHO buses are probably the worst way to see NYC. You end up trapped in traffic sitting on the top of the bus instead of walking along the street and actually doing things. The buses are busy and not frequent enough during the busiest tourist seasons (October is busy). And if the weather is cold or wet, you end up sitting INSIDE the bus, which is the only thing worse than sitting on top of the bus. The best way is to buy a one-week unlimited Metrocard and go to the parts of the city you want to explore.

There are a lot of walking tours out there, but I can't recommend specific ones. I know there are other posters who can. If you are interested in something historical, look at the tours offered by the Lower East Side Tenement Museum.

I agree with Doug, HOHO are overpriced and odd. When I hear them pass, the guide is often giving misinformation. You will learn the subway immediately and then there are buses, walking and taxis as a last resort.

I agree with Doug,

For us, walking is a 1st resort, up to ~10mi per day we find enjoyable. That's the best way to experience the feel, sights, sounds, smells of NYC. Sometimes gritty, sometimes smelly, sometimes loud, but always stimulating. People watching, shopping, stopping in small cafe's you run across, finding new places to come back to, or just enjoying being outside and on the move.

I used this company for walking tours, enjoyed them.

https://freetoursbyfoot.com/new-york...tour-calendar/

HOHO bus is a no-no for the reasons cited above.
Strongly recommend the Original Greenwich Village walking tour with food tastings by Foods of New York. I usually avoid group tours, received this as a gift and loved it.
Also endorse Doug's recommendation for the Tenement Museum

At first, NYC subways can seem confusing and intimidating. Use your subway map (I like paper since it always gets a signal) and don't be afraid to ask. Most people are happy to help. When we went to see my daughter graduate in NYC, my mom, who couldn't navigate the stairs took a cab and it took three times as long as the group who took the subway!

I also recommend the tours at The Tenement Museum on the Lower East Side, but you should be aware that most of the tours are inside. There is one walking tour of the neighborhood.

New York is so big and diverse that you are probably only going to find tours of specific neighborhoods. There are many self-guided tours that you could use.

Some people like the Circle Line tours that go either completely around Manhattan or on a shorter semi-circle route.