For starters, I don't like the "gray grid" that surrounds the page. It is very unappealing especially since you are dealing with food items. In general, the homepage looks disorganized. The layout/design of the page has not been well thought out or constructed.
As a suggestion, I would replicate your store sign (Bagel Junction Deli) exactly like it is in the photo and use it at the top of your page instead of what you have now. I like the photo of your store at the bottom and maybe it could be moved more to the middle of the page.
Importantly, decide on a theme. If it is "Bringing the taste of Olde New York to Newtown" then reflect that more in your choices of type style, color, graphics and photos throughout the page to tie it together.
Also, decide what is most important in your mind to promote on the page and adjust those elements accordingly. Your menu has a lot to offer and right now the design of the page is a jumble and not reflecting that. You don't know where to look first.
I don't like the scrolling advertisement across the page.
Your PDF menu should be a full webpage... two reasons. 1. PDFs suck for SEO and 2. PDFs are super slow loading.
The photos you put up should be redone by a professional photographer who specializes in food. The pics that are there, I am certain don't really do your platters justice. Also, being able to search your photos would add to your SEO.
I would have commented on your source code, but I couldn't right click on your pages.
I like the ability to order online and the map. Very useful. Your "delivery area" needs to be delineated though... You might find yourself getting orders from places where you wouldn't otherwise deliver.
I think the "daily updates" button should be called "Today's Specials" or something slightly more relevant.
And oddly enough, as a specialist in "pepper", I completely disagree with your comment about "pepper". If you are talking about peppercorns, then I don't necessarily have a problem with it but ground pepper, like coffee, starts losing its flavour the second you grind it. A bit pedantic, I know, but I personally think you should make the distinction.
Who is Chef Jason? Is he you, or your chef? If you're going to quote him, you should tell us who he is. In addition to that, I would talk about his specialties and what makes him such a great chef.
Finally... who are you? Who runs the shop, who works there... It's a local targeting website... Get personal. I want to know Mom and Pop, it makes it that much easier to order from you, when we're "friends".
You have a nice start, but there is much room for improvement. The color palate is not working. There is too much text that make it look like a word document, not an interactive site. The text is what I call "happy talk" where you talk about the business too much and not enough about what people are on the website to find out. The "call to action" buttons such as "sign up for a free lunch" "guestbook" and daily updates are seemingly haphazardly placed without much thought. The page does not flow well, meaning that it is not clear where a new visitor is to look first, second third... The entire site appears to have been designed by template.