You could search for USB tokens based on NXP P5CT072 chip (2003) - this chip supports USB 2.0 interface

Specs:

NXP P5CT072 chip data sheet

Another candidate - NXP JCOP 41 (JCOP41)

Some relevant links about USB in JCOP41:

feedback on JCOP 41 via USB interface

Specs:

yet one more USB SE - NXP p5cu036

Specs:

Here is another chip from STi - ST23YT66 - Smartcard MCUwith USB and SPI interfaces and 66 KBytes EEPROM. This chip has been used in Ledger bitcoin wallet, and in some FIDO U2F tokens

Specs for ST23YT66 chip

More STi chips from ST23 family

The ST23YT66 product is a serial access microcontroller specially designed for secure smartcard applications. It is based on an enhanced STMicroelectronics 8/16-bit CPU core offering 16 Mbytes linear addressing space. It is manufactured using an advanced highly reliable ST CMOS EEPROM technology. The ST23YT66 is a secure USB microcontroller based on the ST23 core architecture. Its high security level and versatile communication interfaces address user identification functions for computer or network access or for computer-based local or remote applications. The ST23YT66 features a USB full-speed interface for communication with computers as well as various I/Os and an SPI bus for user interfaces (keyboards, displays, etc.).

WARNING: JavaCard is nowhere mentioned, and it looks like this chip has a proprietary dev environment:

Development environment

Development tools for smartcard products include a complete range of hardware systems and software tools from STMicroelectronics and third-party tool suppliers. The range of tools includes solutions to help you to develop and debug your application and evaluate smartcard products and their peripherals. An Integrated Development Environment (IDE), the ST Visual Develop (STVD), provides a set of tools for developing embedded applications. This interface manages the project configuration, code edition, code generation and program debugging. A Smartcard ICS emulator (SCICS) is available for developing and validating your application code. All the information needed to generate the application code and personalization will be collected in a delivery file (.DLV extension). This file is created using the Delivery menu of the STMicroelectronics configuration software tool, SCOOL.

Here are USB token chips from Infineon:

Infenion SLE 78 SOLID FLASH family of chips

Also, Atmel ATECC508A , older AT90SC6464C-USB (2001)

And by the way, Atmel Corporation is headquartered in San Jose, California

ACS - USB Token with Secure Element - TSP-CryptoMate64

Tech Specs

It is based on the same chip as this ACS card

Looks like some sort of secure element exists in these USB dongles from Century Longmai Technology Co (HK) :