For each doctor pick the best monster that was introduced for that doctor.

9th doctor - The gasmask children

10th doctor - weeping angels

11th doctor - the silence

In order:

Daleks (yes, better than Cybermen)
Yeti
Silurians (yes, better than Sontarans)
Zygons
Mara
Ummm, Vervoids?
Haemovores
[not applicable]

Then I basically agree with you. Though Eccleston's Reapers were good too.

9th doctor - The gasmask children

10th doctor - Family of Blood

11th doctor - The Silence

1st - Daleks

2nd - Yeti

3rd - Sea Devils

4th - Mandrels

5th - Mara

6th - Vervoids

7th - Haemovores

8th - None.

9th - Slitheen

10th - Weeping Angels

11th - Silence

That is EXACTLY what I thought!! Amazing!

This is not quite the question the OP asked but I always thought you could assign the big 4 to one each of the first Doctors:

1st - Daleks
2nd - Cybermen (I know they debuted in Hartnells last story, but I feel like they belong more to Troughton's era)
3rd - The Master
4th - Davros

In terms of what the OP actually asked, I would say the Great Intelligence rather than the Yeti (actually I think the Yeti are a little cuddly and ridiculous) for the Troughton era.

For the 6th Doctor, surely Sil is the defining 'monster' original to his era?

The Master as a Snake is surely 8's best enemy

The Doctor's worst new enemies per Doctor:

1st - The Daleks.

2nd - The Great Intelligence.

3rd - The Master.

4th - The Zygons.

5th - Mara.

6th - Vervoids.

7th - Haemovores.

8th - Low American Ratings.

9th - The gasmask children.

10th - Weeping Angles.

11th - The Silence.