Yes, stem cells can pass through blood vessels and capillaries (as @WYSIWYG points, these cells should be small enough to fit inside that capillary). The interesting thing is that they posses multiple mechanisms of transmigration. They are attracted by TNF-alpha activated endothelial cells  and can pass through by :
- leukocyte-like diapedesis
- paracellular migration between endothelial cells
- transcellular, directly through individual endothelial cells
I am thinking of some type of encapsulated stem cells where ultrasound, heat or magnetic fields from the MRI would break up the encapsulation releasing the stem cell at the targeted area.
Note: I don't know if the following is plausible. It is just something I thought of and I consider it to be more effective than what you suggested.
Then what is the purpose of using stem cells that are capable of chemotactic movements and can go by themselves in targeted areas? The encapsulation you propose could be used to fit inside the cell a drug-containing capsule that would break upon external electromagnetic, ultrasonic (etc.) stimulation. This means that the capsule would also contain a substance capable of inducing cytoplasmic membrane lysis, so the drug could reach the interstitial space. Or the cell could be genetically engineered to secrete that drug, when available in cytoplasm, through exocytosis.
But why not get rid of that capsule? A cell could contain (for example) a cytostatic drug in its cytoplasm and also be fitted with membrane receptors for a specific tumoral marker. When it reaches the tumor, receptor stimulation should trigger exocytosis of drug.
- Teo GS, Ankrum JA, Martinelli R, Boetto SE, Simms K, Sciuto TE, Dvorak AM, Karp JM, Carman CV. Mesenchymal stem cells transmigrate between and directly through tumor necrosis factor-α-activated endothelial cells via both leukocyte-like and novel mechanisms. Stem Cells. 2012 Nov;30(11):2472-86. doi: 10.1002/stem.1198. PubMed PMID: 22887987.