I feel like I have gone through the mill with my Colchester school decisions. So I hope my experience might give you some insight.
Unfortunately I can't comment on St Thomas'.
We sent our children to Oxford house without researching it properly, in hindsight! It's a small school, and works the kids incredibly hard and gets their education way up above other schools but you have to be prepared for the commitment. If your focus for secondary is the Grammar, then your best option is to put them in Oxford House as they will get amazing results. But be prepared for the work to encroach quite a bit into your family life. In year 3, (age 7), 1 hour a night of homework is not uncommon, 7 days a week. If your child is not bright it will be a tough journey and will have an impact on holidays (they still get homework) and weekends. We had a bright one and a sporty one. However it depends what type of family you are... if you believe in extra tutoring and putting homework before playdates, hobbies, then you may suit it. The point is, the reason why the Oxford House kids get results is that they work so hard. It's poor for sport and the playground is small. Very strict, but the kids seem to adapt well however sometimes the rules of not talking during lunch or walking to assembly with hands behind your back in silence, seems overly archaic. Traditional, verging on old fashioned with no male teachers, but they produce very nice kids with a very strong work ethic and well behaved.
Holmwood House is where we would have sent them. It's a great school and the extra curricular element of the school is amazing. We really liked the headmaster, the school's philosophy and the kids will get a great rounded education without the pressure of the 11+ that you will get at Oxford House. Your journey to Holmwood House would be fine, just bomb down the A120, its actually much easier than getting to Oxford House, which by the way has the most awful parking capacity - basically there is none and its a bun fun every am and pm. We came from much further than wivenhoe into Colchester.
I hear good reports about Little Garths as its an all round nice school.
In the end we moved our kids to Ipswich school. We looked at Colchester High, St Philomenas in Frinton, RHS, St Josephs and Ipswich School for girls. our kids were older than yours by the time we made the decision, and yes the bus ride is Epic for them, but they love it and we have seen them blossom as children and spread their wings.
In hindsight I would have picked Holmwood House and then at the point where they were old enough for the bus, 11 or 13, send them to Ipswich school as boarding was never an option for us, emotionally or financially!
Good luck. It's a hard topic to advise on because all kids, all parents, all families are different and what's right for someone may not be right for someone else... But this was our personal experience.