The first part is just:

GatherBy[data, Last]

You'll have to explain in more detail what you mean by:

How do I test whether these two data sets are linearly independent?

The first part is just:

GatherBy[data, Last]

For easy manipulation you might use this:

ruleData= #[[1, -1]] -> # & /@ GatherBy[data, Last];

Then get the part you want with e.g.:

4 /. ruleData

{{41, 49.32, 4}, {41, 48.21, 4}, {47, 48.87, 4}, . . .}

You'll have to explain in more detail what you mean by:

How do I test whether these two data sets are linearly independent?