Lake Kawaguchi is a great day trip from Tokyo although very long, so my tip would be to book up a night somewhere and enjoy the lush scenery and the beautiful lake and some of the many activities around the area too.
In my top 3, we have a dog-friendly place, a Lee-friendly (me!) place and a ryokan for that extra special treat!
Lakeside Cottage (Dog friendly)
We took our dog once to Lake Kawaguchi (he loved it by the way!) so we needed a pet friendly place to stay that was reasonable.
The cottages are a 15-20 minute drive from station.
Prices are reasonable off season and like many other places, climb with the number of visitors.
The cottages are on the east side of the lake so Mount Fuji is behind you and you cannot see it at all. But the views are lovely and the walking path way is easily accessible, so do not be put off.
The office is in the shop and there is plenty of fishing gear available to buy/rent as it is a main activity of the area. I am sure they can help with boat rentals too.
Inside is nice enough. There is a gas range, along with a rice cooker and aside from a few stink bugs in the vicinity, cooking was very pleasant.
Prices can be reasonable - around ¥15,000 per cottage with 2 adults, but it may change according to season.
Check online - http://www.lakesidecottage.jp/
Komaya Ryokan (Just about perfect!)
Komaya is by far our favourite hideout. If you are coming from the big city, this hotel provides the perfect respite.
We like to walk across as there IS a pathway ( do NOT be put off by people trying to tell you otherwise or dissuade you - we LOVE this walk!)
The hotel is opposite Mount Fuji and if you ask for a lakeside room, you will be spoilt with views of my favourite mountain!
On your arrival there are cookies and tea. What more could you want!
Breakfast is traditional Japanese style with natto and rice. You should try it!
This hotel is reasonable and actually calling direct is a tiny bit cheaper than Booking.com if you can manage it!
No website - old school!
OOOOH.....Must not forget - this hotel has two private onsens (which means tattoos OK!!!) Just book a time slot on arrival and it is yours for one hour! (If you are sharing a room with friends, you can share the one hour time slot if not visiting the onsen together.
Mizuno Hotel (A little bit fancy!)
This is a good choice if you want to impress a visitor to Japan and show them the full works. The food is beautifully over-the-top, but be sure your guest has the palate for it all. Locally sourced fish, cooked and raw, will be part of the selection. It's a unique experience.