Kyoto to Tokyo from April 24th to April 29th 2019


We have our AirBnb stay in Tokyo (Asakusa Station Area) from April 24th to April29th. Our departing Airport is in Haneda Airport on April 29th. 

I wanted to ask when is the best time to leave from Kyoto going to Tokya Asakusa Station. We also want to explore the Asakusa Area on that day. 

We are a family of 4 (my husband and 2 young boys). We wanted to explore Tokyo but not the Disney Tokyo. 

We also want to go to Nikko for a day trip while in Tokyo. 

Any recommendation that would be enjoyable for all of us while in Tokyo area? 

Ghilbi Museum?

Tokyo Light Museum?

One Piece Tokyo tower and Joypolis?

What is the best and cheapest way to go by Metro or bus and also to utilized a lot of time day by day. 

Thank you for taking so much time to look into my question. :-)