I'm sorry for your loss.

Kudos for everyone's posts thus far.
Very insightful and thoughtful.

Though Canadian, I've been living and working in Japan for 13 years now, and since my wife is Japanese, I've attended a number of funerals or death anniversary ceremonies of both relatives and business associates.

So, may I offer a few tips based on these assumptions:
I'm guessing from your posts that you are not in Japan, but will be at some point in the future, and will visit both the workplace and home of the deceased.

1) You mention the company you work for, so if you are in a position to approve or request the use of company funds, money is the correct gift to present - with all the earlier provisos about the notes being clean, avoiding combinations of 4, ensuring the amount represents the depth of your business relationship, placing it in the proper funerary envelope, etc. This can be done in person when you next visit Japan. It is true that these monetary gifts are usually presented at the funeral, but given the international nature of the relationship, any gift will be seen as touching and thoughtful, and not as being late.

2) Sitting "seiza" [knees tucked under] - if possible - while offering the incense and a moment of silent reflection while seeing the deceased's photo is key to showing respect for the deceased and family at the family's altar located inside their reception room - which might be their everyday living room or their seldom used "traditional" tatami-matted room. IME it is always 3 incense sticks that are lit and lain on their side in a long, ceramic incense holder.

3) It is fine to speak of the deceased with her survivors - what her good qualities were and something personal you remember of her.

4) Unless you are very familiar with what the deceased's favourite drink or food was, I'd hold off bringing that type of offering. Often one finds family members regularly renew these offerings, but without that intimate knowledge, your gift might be accepted as just a regular omiyage [gift] from abroad.

It is especially moving to see as an offering for a deceased child his/her favourite toy, food or drink, even many years after the death - they remain forever at that age. I have 2 young sons and it really gets to me...

Another observation is that the switch to turn on the cremation oven is turned on by the closest family member - they are forced to admit and accept the death in the most upfront of ways, even before the handling and preparing of the bones for burial.

As always, death and how we deal with it across cultures is a fascinating, if saddening, thing.