My rule of thumb for booking “reasonable” accommodation in Japan is ¥10,000 per night for two. In cities, this is sufficient for a clean if often cramped “business hotel” room for two. In the countryside, this is enough for almost all minshuku (inn/B&B) accommodation, perhaps the lower tiers of ryokan as well if you skip meals/dinner. (Note that many ryokan charge per person, not room, so read the fine print.)
While there is obviously a lot of variation, there’s generally less of it than in (say) the US, where it’s not unusual for a room to cost 5x more at the “wrong” time. Many hotels still publish a rate calendar that lets you work out well in advance the best/cheapest times to go.
Central Tokyo tends to be more expensive than the rest of the country, but it’s not hard to find cheaper digs if you look for outlying/less fashionable areas like Ueno. The main pitfalls tend to be Japanese long holidays (Golden Week in late April, Obon in August, New Year’s), plus seasonal destinations like ski resorts in winter, Hokkaido in the summer and Kyoto in cherry blossom season. The big cities have tons of accommodation options and are virtually never sold out, even during these peak seasons, since the increase in tourists is more than matched by the drop in business travel.
For booking hotels, don’t use usual Western players, but use local sites Rakuten Travel and Jalan instead, since they have much better selections and access to promotional pricing. More tips at Wikivoyage: https://en.wikivoyage.org/wiki/Japan#Sleep