I tried having Minecolonies farmer and rats to harvest, but they dont recognize the crops.

Tomatoes might receive a strategic redo later down, to address both sides of this issue.
I'll be closing it for now, but it's marked for consideration. Thanks for the help!

Also straw golems

Sorry about the above user's spam content, I deleted the messages.

As for the issue: are you planting crops above Rich Soil? Compatibility issues can arise on these interactions, and there's a possibility some mods don't recognize Rich Soil Farmland as a valid ground for farming. I'll do some testing later.

No I was planting them on vanilla farmland

@kihgy Sorry for the delay.

I need further info to check on this issue. Please provide your mod list (including FD and Forge), and answer the questions below:

1. Are these farming methods not recognizing tomatoes in particular, or are they failing with every crop?
2. Can they interact with the upper side of Rice crops?

I checked with some MineColonies users, and the only crop that seems to fail is the tomato, which is expected. If all crops are failing, I need to check further.

I ran some tests on the mods for both this issue and #227, and it largely boils down to these mods requiring crops to be instanceof CropsBlock rather than checking for their age and IGrowable. Unfortunate...

Rats: They glitch out trying to break tomatoes and the underside of Rice, causing a rapid seed duplicating glitch. Might be more on their end, though;
MineColonies: The crop needs to be textbook like a vanilla crop for Farmers to make use of them. I haven't tested Planters yet, though I expect them to not work with Tomatoes, Rice or Sweet Berries.
PneumaticCraft: Works with Rice, ignores Tomatoes.

Again, this is an issue, as making Tomatoes a CropsBlock makes simple-harvesting mods disrupt their plucking mechanic. Though in this case, the trade-off is very large; being able to auto-farm Tomatoes matters more. I might convert them back to a CropsBlock sometime.