Three days would be too short to explore both Osaka City and Kyoto City.
Unless you have a special reason to be in Tokyo during the daytime on Day 5 (Sunday, April 8), it sounds better to leave Osaka or Kyoto in the afternoon | evening or to stay there for another night.
Major tourists spots in Kansai Region may be crowded on the weekend from the evening of Day 3 (Friday, April 6) to the night of Day 5 (Sunday, April 8).
Especially when cherry blossoms fully bloom, popular cherry viewing sites may attract many visitors.
Maybe you on Day 2 (Thursday, April 5), which will be a normal weekday, can enjoy the cherry blossom viewing event hosted by Japan Mint at its headquarter site in Osaka City.
This yearly event is held for 7 days; currently the schedule for spring 2018 is not yet announced.
https://www.mint.go.jp/eng/enjoy-eng/sakura-eng/toorinuke-engAs your transportation mode,
you might hope to have domestic flights at discount fares (about 8000 yen per person per way)
from Narita (NRT) either to Osaka Itami (ITM) in the evening of Day 1 or to Kansai (KIX) in the late morning of Day 2
and back from Osaka Itami (ITM) to Tokyo Haneda (HND) on Day 5.
- ANA Experience JAPAN Fare
https://www.ana.co.jp/en/us/promotions/share/experience_jp/Staying in Hotel Sunroute Plaza Shinjuku Sunroute hotel chain has two hotels around (JR) Shinjuku Station.
When you take a taxi, you indicate "Sunroute Plaza" clearly.
Narita Getaway Hotel The name of this hotel seems to be Narita Gateway Hotel, not "Gataway" (!!) hotel.