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1) Select your polygon of interest - you can do this manually or with one of the selection tools.
2) Select your 'marginal' points using the Select By Attributes tool with the Method drop-down set to 'Add to current selection'.
You will now have a selected polygon in one layer and selected points in another layer.
3) Use the Select By Location tool to ...
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To summarize the very useful comments by @Spacedman, @JeffreyEvans and @AriB.Friedman, but also to address the questioner's second problem about saving the generated subset and to provide a reproducible example for future audience, let me add a brief example to cover the whole topic. In fact, I'm much more often working with raster data than point or polygon ...
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If you are using ArcServer 10.1 you could create a Geoprocessing service which references either a model or script that you built to do this.
The link above gives step by step instructions on how to create the model, then create the services and finally consume it in your app.
Alternatively, there is this sample that uses a query to select records, you ...
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