How to cluster government census data in order to group Metropolitan statistical areas
If you want to identify the distance between MSAs. Then yes, I think it would be best to first aggregate your features such that each instance (row) represents an MSA. From there you will have an $n\times m$ matrix where $n$ is the number of MSA, and $m$ is the number of features you end up with.
You can then apply your clustering algorithm, there are many to choose from, among my favorites I always try are:

K-means
K-nearest neighbors
Spectral clustering
DBSCAN

Others can be found here.
Once you train the clustering algorithm then you will get an associated cluster values for each of the $n$ rows in your input matrix. With this you will know what MSAs are similar in nature given the selected set of features.