site1 <- selectInput(
    inputId = "site1",
    label = "Select a first site:",
    choices = siteChoices
    )

<select id="site1" name="sites[site1]"><option value="9" selected>Liberty E  -  9</option>
<option value="13">Liberty S  -  13</option>
<option value="18">New Milford E  -  18</option>
<option value="21">Dimock S  -  21</option>
</select>

alert($("#site1").html());

<option value="9" selected="selected"></option>

<option value="9" selected="selected">Liberty E  -  9</option>