Everyone shoots sensoji temple and shibuya crossing but they're packed by 9am. Better tokyo spots for golden hour shots:

Ueno park around shinobazu pond at 6am. Gorgeous reflection shots of bentendo temple with zero people. The lotus flowers in summer create incredible foreground frames.

Tokyo station marunouchi red brick building just after sunrise. That meiji-era architecture with empty chiyoda streets looks like a movie set. JR security won't bother you if you're respectful.

Sumida river from asakusa bridge early morning. You get tokyo skytree, traditional yakatabune boats, and morning light on the water. Way better than the crowded sky tree observation decks at ¥3000.