Tokyo-Mt Fuji-Hakone-Kyoto without JR Pass

We are planning to travel April next year from Tokyo to Mt Fuji - stay a night in Hakone and travel to Kyoto.
Can you please explain what's the convenient ways to travel if we didn't buy the JR Pass and how much they will cost.
Is there any tour cater from Tokyo - Mt Fuji - Hakone only, as we will continue to Kyoto?

Post your full itinerary so we can figure it out.

How to travel between Tokyo and Mount Fuji (Fuji Five Lakes):
http://www.japan-guide.com/e/e6905.html

How to travel between Mount Fuji and Hakone:
http://www.japan-guide.com/e/e6905.html?aFROM=5200_6900

How to travel between Hakone and Kyoto:
http://www.japan-guide.com/e/e5206.html?aFROM=2158_5200

If a low budget is important for you, then it may be best to return to Tokyo once after visiting Mount Fuji and Hakone and take a discount overnight bus from Tokyo to Kyoto.

How to travel between Tokyo and Kyoto:
http://www.japan-guide.com/e/e2363.html

Is there any tour cater from Tokyo - Mt Fuji - Hakone only, as we will continue to Kyoto?

I am not aware of it.

Thank you for your prompt respond.
My itinerary:
- day 1: Tokyo
- day 2: Disneyland
- day 3: around Tokyo
- day 4: travel to Mt Fuji stay 1 night in Hakone
- day 5: travel to Kyoto stay 1 night in Kyoto
- day 6: travel to Osaka stay 2 nights in Osaka
- day 7: around Osaka
- day 8: fly back to Melbourne from Osaka

We only have 1 week to spend in Japan and we want to stay 1 night in Hakone. Could you please advise the best way to travel as we will travel with my 2 boys, ages 7 and 10.
Thanks in advance for your advice.

Since you're flying out of Kansai, don't bother with the JR Pass. Just buy the regular tickets.

Pls advise if dun use JR pass, what is a regular ticket?

Use Hyperdia for fares, timetables and routes.