This is our first time travelling to Japan, we want to visit 3 main cities Tokyo, Kyoto and Osaka.You don't seem to have any time budgeted for Tokyo itself. I'd recommend cutting down on the side trips and spending 2-3 days exploring the city.
Day 1 (Feb 29): Arrival Narita at 10:35am then transfer to Shinjuku or Asakusa, still not sure where we staying, can you give me suggest, our budget 50-80$ per night?. We will walk around Sensoji, Skytree and somewhere at afternoon and evening.Check booking.com and agoda, you're likely to find something in your budget around either area, but more likely on the Asakusa side of Tokyo.
Day 2 (Mar 01): Tokyo to Nikko (Day trip). Is it worth to see or not? Can i combine with other places?Nikko is great. I'd probably keep it over Kamakura if you have to drop something. It's hard to combine with anything on a daytrip. Maybe Kinugawa Onsen if you do an overnight, but your itinerary is a little packed.
Day 3 (Mar 02): One day for Disneyland/sea. Which one is better?Disneysea is unique, however if this is your first time to any disney then disneyland is the more classic destination.
Day 4 (Mar 03): Kamakura to see the big buddha. We need to stay overnight here or go back Tokyo? Can i combine go to Yokohama also?Daytrip is best and easily combined with Yokohama... however I would also consider dropping both of these since you'll also be spending time in Kyoto and Tokyo are basically the same attractions, but bigger and better (probably gonna get some negative feedback with that comment though ;)
Day 5 (Mar 05): Mt. Fuji, we want to see/view Mt Fuji, which place (Hakone or Kawaguchiko) is good to see Mt Fuji and stay overnight? And how to go to Mt. Fuji from there? We don't climbing or trekking.Kawaguchiko is better because there are higher percentages of seeing the mountain. But if seeing the mountain isn't the biggest priority then maybe Hakone would be more enjoyable. Either are easy sidetrips from Tokyo, or done along the way to Kyoto.
Day 6 (Mar 06): Nagoya (How many day is good to stay at Nagoya? 1 or 2 days before go to Shirakawago? Is it worth to stay at Nagoya one night?As much as I like Nagoya, I'd recommend skipping it for time.
Day 7 (Mar 07): Shirakawago. We want to see the snow and walk around this place so one night is good for stay at here?Yes, definitely book a minshuku at one of the farmhouses. And do it asap, as they are booking out fast this year.
Day 8 (Mar 08): Kyoto- Where we need to go or see?http://www.japan-guide.com/e/e3950.htmlDay 9 (Mar 09): Nara day trip and go back KyotoVisit Todaiji to get a giant Buddha experience
Day 10 (Mar 10): Kyoto
Day 11(Mar 11) :Osaka (still not sure where to go, maybe Hiroshima).
Day 12 (Mar 12): Kobe day trip. We need how long to walk around here? Can we combine with other places?Hard to say. I'd either do Osaka and Kobe, or skip it for something like Himeji Castle and Hiroshima. Or skip both to add a day to Kyoto and a daytrip to Himeji Castle.
I still have some confuse about JR pass? May i ask JR pass can use for JR line inside Tokyo and JR from Narita to Tokyo? What's kind JR pass need to book?You can use it for the Narita Express, however overall the pass is not going to pay off for your itinerary as it stands. Regular tickets will be cheaper.
Is it the itinerary cramped?I think so. You may have to drop some stuff to open it up.