luggage send-ahead clarification

we'll be at a Tokyo hotel and then visiting friends nearby for a few days before we take the train to Kyoto. I know we can send luggage from the hotel, but my question remains is there a place at Kyoto train station where luggage can be sent to that will hold it for 3 days

Why send it to the train station, when you can send it directly to the hotel? You can specify a delivery date, and the delivery service can hold it for a few days in between.

we're staying at an un-attended machiya in Kyoto so there's no one there to accept luggage being sent ahead. We're looking for someplace in Kyoto where we can have luggage sent ahead before we arrive by train.

I see. There is a takuhaibin counter inside Kyoto Station, directly next to the luggage storage counter, which might accept deliveries. Alternatively, the delivery companies have service and distribution centers throughout Japan, including Kyoto City, where you can send luggage to. So, when in Tokyo, I recommend to call the delivery service and consult:
http://www.kuronekoyamato.co.jp/english/index.html