Welcome to my country!
Your itinerary itself seems to be well-planned.
One thing I can suggest for improvement is that it sounds better to allot more time for Kanazawa City.
Please note that bus rides on the section between Shirakawa-go and Kanazawa Station requires reservation. http://www.japan-guide.com/bus/shirakawago.html
A few possible problems are
: Your six days until May 7 will be during the Golden Week period in 2017 (from April 29 through May 7); some popular tourist spots may be crowded with visitors.
: Your baby, while carried around by railroad or bus, may cry….
Have you made an appointment to stay in the temple on Mount Koya?
What stations are close to your accommodations in Osaka City, Kyoto City, Takayama City, Kanazawa City and Tokyo Metropolis?
Which airport will you fly out from, Haneda Airport [HND] or Narita Airport [NRT]?
(Narita Airport is located actually outside Tokyo.) Tokyo with possible one day trips to Kamakura, Nikko and Fuji 5 lakes.
Well, if your main purpose of making the Fuji Five Lakes trip is to have a view of Mount Fuji, you alternatively can visit the Hakone area.
A route which I can suggest for that case is
: Kyoto -- Kanazawa -- Shirakawa-go -- Takayama -- Nagoya -- Odawara -- Hakone -- Odawara -- Tokyo.
In your current order of places, you need about 3 hours at least to get from Kyoto Station to Takayama Station (even when you use the Shinkansen until Nagoya) and about 5 hours to travel from Tokyo to near the Lake Kawaguchiko (among the Fuji Five Lakes) and back.
When you take the above route, you can get from Kyoto Station to Kanazawa Station in around 2 hours 10 minutes and travel from Odawara Station to Hakone-Yumoto Station and back within 1 hour in total.
So, this route seems to be better time-wise.