5 days vacation Tokyo, Kyoto, Osaka Only

Please help me, would JR pass be a better option for the following itinerary?

Arrived in Haneda Airport late night, if im lucky i'll get last train to tokyo or maybe stay at Haneda.

Day 1: Tokyo city tour (Tsukuji fish market, asakusa, Sensoji, Ueno park/Yoyogi park/Taito/inokashira park (Hanami), tokyo skytree)
Day 2: Disneyland/ disney sea, and i plan go to Kyoto with late transportation (bus/shinkansen)
Day 3: Kyoto city tour (Fushimi inari, Kiyomizudera, Sanjusangendo, bamboo forest, Kinkakuji/ kyoto imperial palace, Gion)
Day 4: Kyoto to Osaka, Osaka city tour, depart to Tokyo
Day 5: Tokyo city tour and depart to Haneda (last flight)

Thanks for your answer.