TL;DR: There is no definitive answer to this question.
What should be clarified at the beginning is that even though the realm is often referred to as Seven Kingdoms it is in fact a historical term:
When Aegon I Targaryen embarked on the conquest of the continent from
his seat on Dragonstone he had to contend with seven independent
realms. These were:
- Kingdom of the North
- Kingdom of the Mountain and the Vale
- Kingdom of the Isles and Rivers
- Kingdom of the Rock [later known as the Westerlands]
- Kingdom of the Stormlands
- Kingdom of the Reach
- Principality of Dorne
After the conquest the Kingdom of the Isles and Rivers split into the Iron Islands and the Riverlands and one more region (the Crownlands) was established. As a result, currently the Seven Kingdoms consists of nine regions.
The regions Tywin couldn't have on his mind are the Vale, Dorne, Reach, the Westerlands and the Crownlands because they were not in rebellion at the time. The only region he undoubtedly had on his mind is the North. This means that the other two can be any combination of the remaining three: the Iron Islands, the Stormlands or the Riverlands.
Each possibility can be analysed based on the following criteria:
is the region part of the historical Seven Kingdoms
what are the specifics of the region's rebellion
how important is the region from Tywin's point of view
The Iron Islands:
Balon Greyjoy crowned himself a king, i.e. openly rebelled against
the Iron Throne.
The Iron Islands are generally considered to be one the historical
Seven Kingdoms (due to the fact that it's the inheritor of the
Kingdom of the Isles and Rivers as this kingdom had its origin there
(see Kingdom of the Iron Islands)).
- Balon would probably be considered important by Tywin due to the
fact that The Iron Islands are neightbouring The Westerlands and were
always a big threat for the westermen.
- Tywin does not say this sentence in the book (at least not in his
conversation with Tyrion after the recovery of the latter) and from
the perspective of the first two seasons of the show Balon has almost
no importance. The Iron Islands plot is reduced to just a few scenes
and the fact that there is any rebellion going on there can be
completely missed by the viewers that didn't read the books.
- The Stormlands are undoubtedly one of the historical Seven Kingdoms.
- Stanis Baratheon crowned himself a king, i.e. openly rebelled against
the Iron Throne.
- Stannis just lost an important battle and can be considered (at least
- Stannis control over the Stormlands and the support of the regional
lords is arguable, although regional capital The Storm's End was still in
his hands at the time.
- The Stormlands raised their banners for the King in the North and are
rebelling against the Iron Throne.
- It's the region that is the most affected by the war and would surely
be important for Tywin.
- The Riverlands didn't rebel on its own, but rather joined a
- The Riverlands is not considered a part of the historical Seven
Kingdoms and the distinction is often emphasized, e.g. in this
sentence said by King Robert:
Back in our day, you weren't a real man until you'd fucked one girl
from each of the Seven Kingdoms and the Riverlands.
The above analysis doesn't provide a conclusive answer which regions Tywin had on his mind. We can be sure that one of them is the North. The remaining two can be any combination of the following three: the Iron Islands, the Stormlands or the Riverlands.